2 See the "run control" section for a working example of the
3 syntax to use when making .mdp entries, with and without detailed
4 documentation for values those entries might take. Everything can
5 be cross-referenced, see the examples there. TODO Make more
8 Molecular dynamics parameters (.mdp options)
9 ============================================
16 Default values are given in parentheses, or listed first among
17 choices. The first option in the list is always the default
18 option. Units are given in square brackets. The difference between a
19 dash and an underscore is ignored.
21 A :ref:`sample mdp file <mdp>` is available. This should be
22 appropriate to start a normal simulation. Edit it to suit your
23 specific needs and desires.
31 directories to include in your topology. Format:
32 ``-I/home/john/mylib -I../otherlib``
36 defines to pass to the preprocessor, default is no defines. You can
37 use any defines to control options in your customized topology
38 files. Options that act on existing :ref:`top` file mechanisms
41 ``-DFLEXIBLE`` will use flexible water instead of rigid water
42 into your topology, this can be useful for normal mode analysis.
44 ``-DPOSRES`` will trigger the inclusion of ``posre.itp`` into
45 your topology, used for implementing position restraints.
53 (Despite the name, this list includes algorithms that are not
54 actually integrators over time. :mdp-value:`integrator=steep` and
55 all entries following it are in this category)
59 A leap-frog algorithm for integrating Newton's equations of motion.
63 A velocity Verlet algorithm for integrating Newton's equations
64 of motion. For constant NVE simulations started from
65 corresponding points in the same trajectory, the trajectories
66 are analytically, but not binary, identical to the
67 :mdp-value:`integrator=md` leap-frog integrator. The kinetic
68 energy, which is determined from the whole step velocities and
69 is therefore slightly too high. The advantage of this integrator
70 is more accurate, reversible Nose-Hoover and Parrinello-Rahman
71 coupling integration based on Trotter expansion, as well as
72 (slightly too small) full step velocity output. This all comes
73 at the cost off extra computation, especially with constraints
74 and extra communication in parallel. Note that for nearly all
75 production simulations the :mdp-value:`integrator=md` integrator
78 .. mdp-value:: md-vv-avek
80 A velocity Verlet algorithm identical to
81 :mdp-value:`integrator=md-vv`, except that the kinetic energy is
82 determined as the average of the two half step kinetic energies
83 as in the :mdp-value:`integrator=md` integrator, and this thus
84 more accurate. With Nose-Hoover and/or Parrinello-Rahman
85 coupling this comes with a slight increase in computational
90 An accurate and efficient leap-frog stochastic dynamics
91 integrator. With constraints, coordinates needs to be
92 constrained twice per integration step. Depending on the
93 computational cost of the force calculation, this can take a
94 significant part of the simulation time. The temperature for one
95 or more groups of atoms (:mdp:`tc-grps`) is set with
96 :mdp:`ref-t`, the inverse friction constant for each group is
97 set with :mdp:`tau-t`. The parameters :mdp:`tcoupl` and :mdp:`nsttcouple`
98 are ignored. The random generator is initialized with
99 :mdp:`ld-seed`. When used as a thermostat, an appropriate value
100 for :mdp:`tau-t` is 2 ps, since this results in a friction that
101 is lower than the internal friction of water, while it is high
102 enough to remove excess heat NOTE: temperature deviations decay
103 twice as fast as with a Berendsen thermostat with the same
108 An Euler integrator for Brownian or position Langevin dynamics,
109 the velocity is the force divided by a friction coefficient
110 (:mdp:`bd-fric`) plus random thermal noise (:mdp:`ref-t`). When
111 :mdp:`bd-fric` is 0, the friction coefficient for each particle
112 is calculated as mass/ :mdp:`tau-t`, as for the integrator
113 :mdp-value:`integrator=sd`. The random generator is initialized
118 A steepest descent algorithm for energy minimization. The
119 maximum step size is :mdp:`emstep`, the tolerance is
124 A conjugate gradient algorithm for energy minimization, the
125 tolerance is :mdp:`emtol`. CG is more efficient when a steepest
126 descent step is done every once in a while, this is determined
127 by :mdp:`nstcgsteep`. For a minimization prior to a normal mode
128 analysis, which requires a very high accuracy, |Gromacs| should be
129 compiled in double precision.
131 .. mdp-value:: l-bfgs
133 A quasi-Newtonian algorithm for energy minimization according to
134 the low-memory Broyden-Fletcher-Goldfarb-Shanno approach. In
135 practice this seems to converge faster than Conjugate Gradients,
136 but due to the correction steps necessary it is not (yet)
141 Normal mode analysis is performed on the structure in the :ref:`tpr`
142 file. |Gromacs| should be compiled in double precision.
146 Test particle insertion. The last molecule in the topology is
147 the test particle. A trajectory must be provided to ``mdrun
148 -rerun``. This trajectory should not contain the molecule to be
149 inserted. Insertions are performed :mdp:`nsteps` times in each
150 frame at random locations and with random orientiations of the
151 molecule. When :mdp:`nstlist` is larger than one,
152 :mdp:`nstlist` insertions are performed in a sphere with radius
153 :mdp:`rtpi` around a the same random location using the same
154 pair list. Since pair list construction is expensive,
155 one can perform several extra insertions with the same list
156 almost for free. The random seed is set with
157 :mdp:`ld-seed`. The temperature for the Boltzmann weighting is
158 set with :mdp:`ref-t`, this should match the temperature of the
159 simulation of the original trajectory. Dispersion correction is
160 implemented correctly for TPI. All relevant quantities are
161 written to the file specified with ``mdrun -tpi``. The
162 distribution of insertion energies is written to the file
163 specified with ``mdrun -tpid``. No trajectory or energy file is
164 written. Parallel TPI gives identical results to single-node
165 TPI. For charged molecules, using PME with a fine grid is most
166 accurate and also efficient, since the potential in the system
167 only needs to be calculated once per frame.
171 Test particle insertion into a predefined cavity location. The
172 procedure is the same as for :mdp-value:`integrator=tpi`, except
173 that one coordinate extra is read from the trajectory, which is
174 used as the insertion location. The molecule to be inserted
175 should be centered at 0,0,0. |Gromacs| does not do this for you,
176 since for different situations a different way of centering
177 might be optimal. Also :mdp:`rtpi` sets the radius for the
178 sphere around this location. Neighbor searching is done only
179 once per frame, :mdp:`nstlist` is not used. Parallel
180 :mdp-value:`integrator=tpic` gives identical results to
181 single-rank :mdp-value:`integrator=tpic`.
185 Enable MiMiC QM/MM coupling to run hybrid molecular dynamics.
186 Keey in mind that its required to launch CPMD compiled with MiMiC as well.
187 In this mode all options regarding integration (T-coupling, P-coupling,
188 timestep and number of steps) are ignored as CPMD will do the integration
189 instead. Options related to forces computation (cutoffs, PME parameters,
190 etc.) are working as usual. Atom selection to define QM atoms is read
191 from :mdp:`QMMM-grps`
196 starting time for your run (only makes sense for time-based
202 time step for integration (only makes sense for time-based
208 maximum number of steps to integrate or minimize, -1 is no
214 The starting step. The time at step i in a run is
215 calculated as: t = :mdp:`tinit` + :mdp:`dt` *
216 (:mdp:`init-step` + i). The free-energy lambda is calculated
217 as: lambda = :mdp:`init-lambda` + :mdp:`delta-lambda` *
218 (:mdp:`init-step` + i). Also non-equilibrium MD parameters can
219 depend on the step number. Thus for exact restarts or redoing
220 part of a run it might be necessary to set :mdp:`init-step` to
221 the step number of the restart frame. :ref:`gmx convert-tpr`
222 does this automatically.
224 .. mdp:: simulation-part
227 A simulation can consist of multiple parts, each of which has
228 a part number. This option specifies what that number will
229 be, which helps keep track of parts that are logically the
230 same simulation. This option is generally useful to set only
231 when coping with a crashed simulation where files were lost.
235 .. mdp-value:: Linear
237 Remove center of mass translational velocity
239 .. mdp-value:: Angular
241 Remove center of mass translational and rotational velocity
243 .. mdp-value:: Linear-acceleration-correction
245 Remove center of mass translational velocity. Correct the center of
246 mass position assuming linear acceleration over :mdp:`nstcomm` steps.
247 This is useful for cases where an acceleration is expected on the
248 center of mass which is nearly constant over :mdp:`nstcomm` steps.
249 This can occur for example when pulling on a group using an absolute
254 No restriction on the center of mass motion
259 frequency for center of mass motion removal
263 group(s) for center of mass motion removal, default is the whole
272 (0) [amu ps\ :sup:`-1`]
273 Brownian dynamics friction coefficient. When :mdp:`bd-fric` is 0,
274 the friction coefficient for each particle is calculated as mass/
280 used to initialize random generator for thermal noise for
281 stochastic and Brownian dynamics. When :mdp:`ld-seed` is set to -1,
282 a pseudo random seed is used. When running BD or SD on multiple
283 processors, each processor uses a seed equal to :mdp:`ld-seed` plus
284 the processor number.
292 (10.0) [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
293 the minimization is converged when the maximum force is smaller
304 frequency of performing 1 steepest descent step while doing
305 conjugate gradient energy minimization.
310 Number of correction steps to use for L-BFGS minimization. A higher
311 number is (at least theoretically) more accurate, but slower.
314 Shell Molecular Dynamics
315 ^^^^^^^^^^^^^^^^^^^^^^^^
317 When shells or flexible constraints are present in the system the
318 positions of the shells and the lengths of the flexible constraints
319 are optimized at every time step until either the RMS force on the
320 shells and constraints is less than :mdp:`emtol`, or a maximum number
321 of iterations :mdp:`niter` has been reached. Minimization is converged
322 when the maximum force is smaller than :mdp:`emtol`. For shell MD this
323 value should be 1.0 at most.
328 maximum number of iterations for optimizing the shell positions and
329 the flexible constraints.
334 the step size for optimizing the flexible constraints. Should be
335 chosen as mu/(d2V/dq2) where mu is the reduced mass of two
336 particles in a flexible constraint and d2V/dq2 is the second
337 derivative of the potential in the constraint direction. Hopefully
338 this number does not differ too much between the flexible
339 constraints, as the number of iterations and thus the runtime is
340 very sensitive to fcstep. Try several values!
343 Test particle insertion
344 ^^^^^^^^^^^^^^^^^^^^^^^
349 the test particle insertion radius, see integrators
350 :mdp-value:`integrator=tpi` and :mdp-value:`integrator=tpic`
359 number of steps that elapse between writing coordinates to the output
360 trajectory file (:ref:`trr`), the last coordinates are always written
365 number of steps that elapse between writing velocities to the output
366 trajectory file (:ref:`trr`), the last velocities are always written
371 number of steps that elapse between writing forces to the output
372 trajectory file (:ref:`trr`), the last forces are always written.
377 number of steps that elapse between writing energies to the log
378 file, the last energies are always written
380 .. mdp:: nstcalcenergy
383 number of steps that elapse between calculating the energies, 0 is
384 never. This option is only relevant with dynamics. This option affects the
385 performance in parallel simulations, because calculating energies
386 requires global communication between all processes which can
387 become a bottleneck at high parallelization.
392 number of steps that elapse between writing energies to energy file,
393 the last energies are always written, should be a multiple of
394 :mdp:`nstcalcenergy`. Note that the exact sums and fluctuations
395 over all MD steps modulo :mdp:`nstcalcenergy` are stored in the
396 energy file, so :ref:`gmx energy` can report exact energy averages
397 and fluctuations also when :mdp:`nstenergy` > 1
399 .. mdp:: nstxout-compressed
402 number of steps that elapse between writing position coordinates
403 using lossy compression (:ref:`xtc` file)
405 .. mdp:: compressed-x-precision
408 precision with which to write to the compressed trajectory file
410 .. mdp:: compressed-x-grps
412 group(s) to write to the compressed trajectory file, by default the
413 whole system is written (if :mdp:`nstxout-compressed` > 0)
417 group(s) for which to write to write short-ranged non-bonded
418 potential energies to the energy file (not supported on GPUs)
424 .. mdp:: cutoff-scheme
426 .. mdp-value:: Verlet
428 Generate a pair list with buffering. The buffer size is
429 automatically set based on :mdp:`verlet-buffer-tolerance`,
430 unless this is set to -1, in which case :mdp:`rlist` will be
435 Generate a pair list for groups of atoms, corresponding
436 to the charge groups in the topology. This option is no longer
445 Frequency to update the neighbor list. When dynamics and
446 :mdp:`verlet-buffer-tolerance` set, :mdp:`nstlist` is actually
447 a minimum value and :ref:`gmx mdrun` might increase it, unless
448 it is set to 1. With parallel simulations and/or non-bonded
449 force calculation on the GPU, a value of 20 or 40 often gives
450 the best performance.
454 The neighbor list is only constructed once and never
455 updated. This is mainly useful for vacuum simulations in which
456 all particles see each other. But vacuum simulations are
457 (temporarily) not supported.
467 Use periodic boundary conditions in all directions.
471 Use no periodic boundary conditions, ignore the box. To simulate
472 without cut-offs, set all cut-offs and :mdp:`nstlist` to 0. For
473 best performance without cut-offs on a single MPI rank, set
474 :mdp:`nstlist` to zero and :mdp-value:`ns-type=simple`.
478 Use periodic boundary conditions in x and y directions
479 only. This works only with :mdp-value:`ns-type=grid` and can be used
480 in combination with walls_. Without walls or with only one wall
481 the system size is infinite in the z direction. Therefore
482 pressure coupling or Ewald summation methods can not be
483 used. These disadvantages do not apply when two walls are used.
485 .. mdp:: periodic-molecules
489 molecules are finite, fast molecular PBC can be used
493 for systems with molecules that couple to themselves through the
494 periodic boundary conditions, this requires a slower PBC
495 algorithm and molecules are not made whole in the output
497 .. mdp:: verlet-buffer-tolerance
499 (0.005) [kJ mol\ :sup:`-1` ps\ :sup:`-1`]
501 Used when performing a simulation with dynamics. This sets
502 the maximum allowed error for pair interactions per particle caused
503 by the Verlet buffer, which indirectly sets :mdp:`rlist`. As both
504 :mdp:`nstlist` and the Verlet buffer size are fixed (for
505 performance reasons), particle pairs not in the pair list can
506 occasionally get within the cut-off distance during
507 :mdp:`nstlist` -1 steps. This causes very small jumps in the
508 energy. In a constant-temperature ensemble, these very small energy
509 jumps can be estimated for a given cut-off and :mdp:`rlist`. The
510 estimate assumes a homogeneous particle distribution, hence the
511 errors might be slightly underestimated for multi-phase
512 systems. (See the `reference manual`_ for details). For longer
513 pair-list life-time (:mdp:`nstlist` -1) * :mdp:`dt` the buffer is
514 overestimated, because the interactions between particles are
515 ignored. Combined with cancellation of errors, the actual drift of
516 the total energy is usually one to two orders of magnitude
517 smaller. Note that the generated buffer size takes into account
518 that the |Gromacs| pair-list setup leads to a reduction in the
519 drift by a factor 10, compared to a simple particle-pair based
520 list. Without dynamics (energy minimization etc.), the buffer is 5%
521 of the cut-off. For NVE simulations the initial temperature is
522 used, unless this is zero, in which case a buffer of 10% is
523 used. For NVE simulations the tolerance usually needs to be lowered
524 to achieve proper energy conservation on the nanosecond time
525 scale. To override the automated buffer setting, use
526 :mdp:`verlet-buffer-tolerance` =-1 and set :mdp:`rlist` manually.
531 Cut-off distance for the short-range neighbor list. With dynamics,
532 this is by default set by the :mdp:`verlet-buffer-tolerance` option
533 and the value of :mdp:`rlist` is ignored. Without dynamics, this
534 is by default set to the maximum cut-off plus 5% buffer, except
535 for test particle insertion, where the buffer is managed exactly
536 and automatically. For NVE simulations, where the automated
537 setting is not possible, the advised procedure is to run :ref:`gmx grompp`
538 with an NVT setup with the expected temperature and copy the resulting
539 value of :mdp:`rlist` to the NVE setup.
547 .. mdp-value:: Cut-off
549 Plain cut-off with pair list radius :mdp:`rlist` and
550 Coulomb cut-off :mdp:`rcoulomb`, where :mdp:`rlist` >=
555 Classical Ewald sum electrostatics. The real-space cut-off
556 :mdp:`rcoulomb` should be equal to :mdp:`rlist`. Use *e.g.*
557 :mdp:`rlist` =0.9, :mdp:`rcoulomb` =0.9. The highest magnitude
558 of wave vectors used in reciprocal space is controlled by
559 :mdp:`fourierspacing`. The relative accuracy of
560 direct/reciprocal space is controlled by :mdp:`ewald-rtol`.
562 NOTE: Ewald scales as O(N\ :sup:`3/2`) and is thus extremely slow for
563 large systems. It is included mainly for reference - in most
564 cases PME will perform much better.
568 Fast smooth Particle-Mesh Ewald (SPME) electrostatics. Direct
569 space is similar to the Ewald sum, while the reciprocal part is
570 performed with FFTs. Grid dimensions are controlled with
571 :mdp:`fourierspacing` and the interpolation order with
572 :mdp:`pme-order`. With a grid spacing of 0.1 nm and cubic
573 interpolation the electrostatic forces have an accuracy of
574 2-3*10\ :sup:`-4`. Since the error from the vdw-cutoff is larger than
575 this you might try 0.15 nm. When running in parallel the
576 interpolation parallelizes better than the FFT, so try
577 decreasing grid dimensions while increasing interpolation.
579 .. mdp-value:: P3M-AD
581 Particle-Particle Particle-Mesh algorithm with analytical
582 derivative for for long range electrostatic interactions. The
583 method and code is identical to SPME, except that the influence
584 function is optimized for the grid. This gives a slight increase
587 .. mdp-value:: Reaction-Field
589 Reaction field electrostatics with Coulomb cut-off
590 :mdp:`rcoulomb`, where :mdp:`rlist` >= :mdp:`rvdw`. The
591 dielectric constant beyond the cut-off is
592 :mdp:`epsilon-rf`. The dielectric constant can be set to
593 infinity by setting :mdp:`epsilon-rf` =0.
597 Currently unsupported.
598 :ref:`gmx mdrun` will now expect to find a file ``table.xvg``
599 with user-defined potential functions for repulsion, dispersion
600 and Coulomb. When pair interactions are present, :ref:`gmx
601 mdrun` also expects to find a file ``tablep.xvg`` for the pair
602 interactions. When the same interactions should be used for
603 non-bonded and pair interactions the user can specify the same
604 file name for both table files. These files should contain 7
605 columns: the ``x`` value, ``f(x)``, ``-f'(x)``, ``g(x)``,
606 ``-g'(x)``, ``h(x)``, ``-h'(x)``, where ``f(x)`` is the Coulomb
607 function, ``g(x)`` the dispersion function and ``h(x)`` the
608 repulsion function. When :mdp:`vdwtype` is not set to User the
609 values for ``g``, ``-g'``, ``h`` and ``-h'`` are ignored. For
610 the non-bonded interactions ``x`` values should run from 0 to
611 the largest cut-off distance + :mdp:`table-extension` and
612 should be uniformly spaced. For the pair interactions the table
613 length in the file will be used. The optimal spacing, which is
614 used for non-user tables, is ``0.002 nm`` when you run in mixed
615 precision or ``0.0005 nm`` when you run in double precision. The
616 function value at ``x=0`` is not important. More information is
617 in the printed manual.
619 .. mdp-value:: PME-Switch
621 Currently unsupported.
622 A combination of PME and a switch function for the direct-space
623 part (see above). :mdp:`rcoulomb` is allowed to be smaller than
626 .. mdp-value:: PME-User
628 Currently unsupported.
629 A combination of PME and user tables (see
630 above). :mdp:`rcoulomb` is allowed to be smaller than
631 :mdp:`rlist`. The PME mesh contribution is subtracted from the
632 user table by :ref:`gmx mdrun`. Because of this subtraction the
633 user tables should contain about 10 decimal places.
635 .. mdp-value:: PME-User-Switch
637 Currently unsupported.
638 A combination of PME-User and a switching function (see
639 above). The switching function is applied to final
640 particle-particle interaction, *i.e.* both to the user supplied
641 function and the PME Mesh correction part.
643 .. mdp:: coulomb-modifier
645 .. mdp-value:: Potential-shift
647 Shift the Coulomb potential by a constant such that it is zero
648 at the cut-off. This makes the potential the integral of the
649 force. Note that this does not affect the forces or the
654 Use an unmodified Coulomb potential. This can be useful
655 when comparing energies with those computed with other software.
657 .. mdp:: rcoulomb-switch
660 where to start switching the Coulomb potential, only relevant
661 when force or potential switching is used
666 The distance for the Coulomb cut-off. Note that with PME this value
667 can be increased by the PME tuning in :ref:`gmx mdrun` along with
668 the PME grid spacing.
673 The relative dielectric constant. A value of 0 means infinity.
678 The relative dielectric constant of the reaction field. This
679 is only used with reaction-field electrostatics. A value of 0
688 .. mdp-value:: Cut-off
690 Plain cut-off with pair list radius :mdp:`rlist` and VdW
691 cut-off :mdp:`rvdw`, where :mdp:`rlist` >= :mdp:`rvdw`.
695 Fast smooth Particle-mesh Ewald (SPME) for VdW interactions. The
696 grid dimensions are controlled with :mdp:`fourierspacing` in
697 the same way as for electrostatics, and the interpolation order
698 is controlled with :mdp:`pme-order`. The relative accuracy of
699 direct/reciprocal space is controlled by :mdp:`ewald-rtol-lj`,
700 and the specific combination rules that are to be used by the
701 reciprocal routine are set using :mdp:`lj-pme-comb-rule`.
705 This functionality is deprecated and replaced by using
706 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Force-switch`.
707 The LJ (not Buckingham) potential is decreased over the whole range and
708 the forces decay smoothly to zero between :mdp:`rvdw-switch` and
711 .. mdp-value:: Switch
713 This functionality is deprecated and replaced by using
714 :mdp-value:`vdwtype=Cut-off` with :mdp-value:`vdw-modifier=Potential-switch`.
715 The LJ (not Buckingham) potential is normal out to :mdp:`rvdw-switch`, after
716 which it is switched off to reach zero at :mdp:`rvdw`. Both the
717 potential and force functions are continuously smooth, but be
718 aware that all switch functions will give rise to a bulge
719 (increase) in the force (since we are switching the
724 Currently unsupported.
725 See user for :mdp:`coulombtype`. The function value at zero is
726 not important. When you want to use LJ correction, make sure
727 that :mdp:`rvdw` corresponds to the cut-off in the user-defined
728 function. When :mdp:`coulombtype` is not set to User the values
729 for the ``f`` and ``-f'`` columns are ignored.
731 .. mdp:: vdw-modifier
733 .. mdp-value:: Potential-shift
735 Shift the Van der Waals potential by a constant such that it is
736 zero at the cut-off. This makes the potential the integral of
737 the force. Note that this does not affect the forces or the
742 Use an unmodified Van der Waals potential. This can be useful
743 when comparing energies with those computed with other software.
745 .. mdp-value:: Force-switch
747 Smoothly switches the forces to zero between :mdp:`rvdw-switch`
748 and :mdp:`rvdw`. This shifts the potential shift over the whole
749 range and switches it to zero at the cut-off. Note that this is
750 more expensive to calculate than a plain cut-off and it is not
751 required for energy conservation, since Potential-shift
752 conserves energy just as well.
754 .. mdp-value:: Potential-switch
756 Smoothly switches the potential to zero between
757 :mdp:`rvdw-switch` and :mdp:`rvdw`. Note that this introduces
758 articifically large forces in the switching region and is much
759 more expensive to calculate. This option should only be used if
760 the force field you are using requires this.
765 where to start switching the LJ force and possibly the potential,
766 only relevant when force or potential switching is used
771 distance for the LJ or Buckingham cut-off
777 don't apply any correction
779 .. mdp-value:: EnerPres
781 apply long range dispersion corrections for Energy and Pressure
785 apply long range dispersion corrections for Energy only
791 .. mdp:: table-extension
794 Extension of the non-bonded potential lookup tables beyond the
795 largest cut-off distance. With actual non-bonded interactions
796 the tables are never accessed beyond the cut-off. But a longer
797 table length might be needed for the 1-4 interactions, which
798 are always tabulated irrespective of the use of tables for
799 the non-bonded interactions.
801 .. mdp:: energygrp-table
803 Currently unsupported.
804 When user tables are used for electrostatics and/or VdW, here one
805 can give pairs of energy groups for which seperate user tables
806 should be used. The two energy groups will be appended to the table
807 file name, in order of their definition in :mdp:`energygrps`,
808 seperated by underscores. For example, if ``energygrps = Na Cl
809 Sol`` and ``energygrp-table = Na Na Na Cl``, :ref:`gmx mdrun` will
810 read ``table_Na_Na.xvg`` and ``table_Na_Cl.xvg`` in addition to the
811 normal ``table.xvg`` which will be used for all other energy group
818 .. mdp:: fourierspacing
821 For ordinary Ewald, the ratio of the box dimensions and the spacing
822 determines a lower bound for the number of wave vectors to use in
823 each (signed) direction. For PME and P3M, that ratio determines a
824 lower bound for the number of Fourier-space grid points that will
825 be used along that axis. In all cases, the number for each
826 direction can be overridden by entering a non-zero value for that
827 :mdp:`fourier-nx` direction. For optimizing the relative load of
828 the particle-particle interactions and the mesh part of PME, it is
829 useful to know that the accuracy of the electrostatics remains
830 nearly constant when the Coulomb cut-off and the PME grid spacing
831 are scaled by the same factor. Note that this spacing can be scaled
832 up along with :mdp:`rcoulomb` by the PME tuning in :ref:`gmx mdrun`.
839 Highest magnitude of wave vectors in reciprocal space when using Ewald.
840 Grid size when using PME or P3M. These values override
841 :mdp:`fourierspacing` per direction. The best choice is powers of
842 2, 3, 5 and 7. Avoid large primes. Note that these grid sizes can
843 be reduced along with scaling up :mdp:`rcoulomb` by the PME tuning
849 Interpolation order for PME. 4 equals cubic interpolation. You
850 might try 6/8/10 when running in parallel and simultaneously
851 decrease grid dimension.
856 The relative strength of the Ewald-shifted direct potential at
857 :mdp:`rcoulomb` is given by :mdp:`ewald-rtol`. Decreasing this
858 will give a more accurate direct sum, but then you need more wave
859 vectors for the reciprocal sum.
861 .. mdp:: ewald-rtol-lj
864 When doing PME for VdW-interactions, :mdp:`ewald-rtol-lj` is used
865 to control the relative strength of the dispersion potential at
866 :mdp:`rvdw` in the same way as :mdp:`ewald-rtol` controls the
867 electrostatic potential.
869 .. mdp:: lj-pme-comb-rule
872 The combination rules used to combine VdW-parameters in the
873 reciprocal part of LJ-PME. Geometric rules are much faster than
874 Lorentz-Berthelot and usually the recommended choice, even when the
875 rest of the force field uses the Lorentz-Berthelot rules.
877 .. mdp-value:: Geometric
879 Apply geometric combination rules
881 .. mdp-value:: Lorentz-Berthelot
883 Apply Lorentz-Berthelot combination rules
885 .. mdp:: ewald-geometry
889 The Ewald sum is performed in all three dimensions.
893 The reciprocal sum is still performed in 3D, but a force and
894 potential correction applied in the `z` dimension to produce a
895 pseudo-2D summation. If your system has a slab geometry in the
896 `x-y` plane you can try to increase the `z`-dimension of the box
897 (a box height of 3 times the slab height is usually ok) and use
900 .. mdp:: epsilon-surface
903 This controls the dipole correction to the Ewald summation in
904 3D. The default value of zero means it is turned off. Turn it on by
905 setting it to the value of the relative permittivity of the
906 imaginary surface around your infinite system. Be careful - you
907 shouldn't use this if you have free mobile charges in your
908 system. This value does not affect the slab 3DC variant of the long
919 No temperature coupling.
921 .. mdp-value:: berendsen
923 Temperature coupling with a Berendsen thermostat to a bath with
924 temperature :mdp:`ref-t`, with time constant
925 :mdp:`tau-t`. Several groups can be coupled separately, these
926 are specified in the :mdp:`tc-grps` field separated by spaces.
928 .. mdp-value:: nose-hoover
930 Temperature coupling using a Nose-Hoover extended ensemble. The
931 reference temperature and coupling groups are selected as above,
932 but in this case :mdp:`tau-t` controls the period of the
933 temperature fluctuations at equilibrium, which is slightly
934 different from a relaxation time. For NVT simulations the
935 conserved energy quantity is written to the energy and log files.
937 .. mdp-value:: andersen
939 Temperature coupling by randomizing a fraction of the particle velocities
940 at each timestep. Reference temperature and coupling groups are
941 selected as above. :mdp:`tau-t` is the average time between
942 randomization of each molecule. Inhibits particle dynamics
943 somewhat, but little or no ergodicity issues. Currently only
944 implemented with velocity Verlet, and not implemented with
947 .. mdp-value:: andersen-massive
949 Temperature coupling by randomizing velocities of all particles at
950 infrequent timesteps. Reference temperature and coupling groups are
951 selected as above. :mdp:`tau-t` is the time between
952 randomization of all molecules. Inhibits particle dynamics
953 somewhat, but little or no ergodicity issues. Currently only
954 implemented with velocity Verlet.
956 .. mdp-value:: v-rescale
958 Temperature coupling using velocity rescaling with a stochastic
959 term (JCP 126, 014101). This thermostat is similar to Berendsen
960 coupling, with the same scaling using :mdp:`tau-t`, but the
961 stochastic term ensures that a proper canonical ensemble is
962 generated. The random seed is set with :mdp:`ld-seed`. This
963 thermostat works correctly even for :mdp:`tau-t` =0. For NVT
964 simulations the conserved energy quantity is written to the
970 The frequency for coupling the temperature. The default value of -1
971 sets :mdp:`nsttcouple` equal to :mdp:`nstlist`, unless
972 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
973 Verlet integrators :mdp:`nsttcouple` is set to 1.
975 .. mdp:: nh-chain-length
978 The number of chained Nose-Hoover thermostats for velocity Verlet
979 integrators, the leap-frog :mdp-value:`integrator=md` integrator
980 only supports 1. Data for the NH chain variables is not printed
981 to the :ref:`edr` file by default, but can be turned on with the
982 :mdp:`print-nose-hoover-chain-variables` option.
984 .. mdp:: print-nose-hoover-chain-variables
988 Do not store Nose-Hoover chain variables in the energy file.
992 Store all positions and velocities of the Nose-Hoover chain
997 groups to couple to separate temperature baths
1002 time constant for coupling (one for each group in
1003 :mdp:`tc-grps`), -1 means no temperature coupling
1008 reference temperature for coupling (one for each group in
1019 No pressure coupling. This means a fixed box size.
1021 .. mdp-value:: Berendsen
1023 Exponential relaxation pressure coupling with time constant
1024 :mdp:`tau-p`. The box is scaled every :mdp:`nstpcouple` steps. It has been
1025 argued that this does not yield a correct thermodynamic
1026 ensemble, but it is the most efficient way to scale a box at the
1029 .. mdp-value:: Parrinello-Rahman
1031 Extended-ensemble pressure coupling where the box vectors are
1032 subject to an equation of motion. The equation of motion for the
1033 atoms is coupled to this. No instantaneous scaling takes
1034 place. As for Nose-Hoover temperature coupling the time constant
1035 :mdp:`tau-p` is the period of pressure fluctuations at
1036 equilibrium. This is probably a better method when you want to
1037 apply pressure scaling during data collection, but beware that
1038 you can get very large oscillations if you are starting from a
1039 different pressure. For simulations where the exact fluctations
1040 of the NPT ensemble are important, or if the pressure coupling
1041 time is very short it may not be appropriate, as the previous
1042 time step pressure is used in some steps of the |Gromacs|
1043 implementation for the current time step pressure.
1047 Martyna-Tuckerman-Tobias-Klein implementation, only useable with
1048 :mdp-value:`integrator=md-vv` or :mdp-value:`integrator=md-vv-avek`, very similar to
1049 Parrinello-Rahman. As for Nose-Hoover temperature coupling the
1050 time constant :mdp:`tau-p` is the period of pressure
1051 fluctuations at equilibrium. This is probably a better method
1052 when you want to apply pressure scaling during data collection,
1053 but beware that you can get very large oscillations if you are
1054 starting from a different pressure. Currently (as of version
1055 5.1), it only supports isotropic scaling, and only works without
1060 Specifies the kind of isotropy of the pressure coupling used. Each
1061 kind takes one or more values for :mdp:`compressibility` and
1062 :mdp:`ref-p`. Only a single value is permitted for :mdp:`tau-p`.
1064 .. mdp-value:: isotropic
1066 Isotropic pressure coupling with time constant
1067 :mdp:`tau-p`. One value each for :mdp:`compressibility` and
1068 :mdp:`ref-p` is required.
1070 .. mdp-value:: semiisotropic
1072 Pressure coupling which is isotropic in the ``x`` and ``y``
1073 direction, but different in the ``z`` direction. This can be
1074 useful for membrane simulations. Two values each for
1075 :mdp:`compressibility` and :mdp:`ref-p` are required, for
1076 ``x/y`` and ``z`` directions respectively.
1078 .. mdp-value:: anisotropic
1080 Same as before, but 6 values are needed for ``xx``, ``yy``, ``zz``,
1081 ``xy/yx``, ``xz/zx`` and ``yz/zy`` components,
1082 respectively. When the off-diagonal compressibilities are set to
1083 zero, a rectangular box will stay rectangular. Beware that
1084 anisotropic scaling can lead to extreme deformation of the
1087 .. mdp-value:: surface-tension
1089 Surface tension coupling for surfaces parallel to the
1090 xy-plane. Uses normal pressure coupling for the `z`-direction,
1091 while the surface tension is coupled to the `x/y` dimensions of
1092 the box. The first :mdp:`ref-p` value is the reference surface
1093 tension times the number of surfaces ``bar nm``, the second
1094 value is the reference `z`-pressure ``bar``. The two
1095 :mdp:`compressibility` values are the compressibility in the
1096 `x/y` and `z` direction respectively. The value for the
1097 `z`-compressibility should be reasonably accurate since it
1098 influences the convergence of the surface-tension, it can also
1099 be set to zero to have a box with constant height.
1104 The frequency for coupling the pressure. The default value of -1
1105 sets :mdp:`nstpcouple` equal to :mdp:`nstlist`, unless
1106 :mdp:`nstlist` <=0, then a value of 10 is used. For velocity
1107 Verlet integrators :mdp:`nstpcouple` is set to 1.
1112 The time constant for pressure coupling (one value for all
1115 .. mdp:: compressibility
1118 The compressibility (NOTE: this is now really in bar\ :sup:`-1`) For water at 1
1119 atm and 300 K the compressibility is 4.5e-5 bar\ :sup:`-1`. The number of
1120 required values is implied by :mdp:`pcoupltype`.
1125 The reference pressure for coupling. The number of required values
1126 is implied by :mdp:`pcoupltype`.
1128 .. mdp:: refcoord-scaling
1132 The reference coordinates for position restraints are not
1133 modified. Note that with this option the virial and pressure
1134 might be ill defined, see :ref:`here <reference-manual-position-restraints>`
1139 The reference coordinates are scaled with the scaling matrix of
1140 the pressure coupling.
1144 Scale the center of mass of the reference coordinates with the
1145 scaling matrix of the pressure coupling. The vectors of each
1146 reference coordinate to the center of mass are not scaled. Only
1147 one COM is used, even when there are multiple molecules with
1148 position restraints. For calculating the COM of the reference
1149 coordinates in the starting configuration, periodic boundary
1150 conditions are not taken into account. Note that with this option
1151 the virial and pressure might be ill defined, see
1152 :ref:`here <reference-manual-position-restraints>` for more details.
1158 Simulated annealing is controlled separately for each temperature
1159 group in |Gromacs|. The reference temperature is a piecewise linear
1160 function, but you can use an arbitrary number of points for each
1161 group, and choose either a single sequence or a periodic behaviour for
1162 each group. The actual annealing is performed by dynamically changing
1163 the reference temperature used in the thermostat algorithm selected,
1164 so remember that the system will usually not instantaneously reach the
1165 reference temperature!
1169 Type of annealing for each temperature group
1173 No simulated annealing - just couple to reference temperature value.
1175 .. mdp-value:: single
1177 A single sequence of annealing points. If your simulation is
1178 longer than the time of the last point, the temperature will be
1179 coupled to this constant value after the annealing sequence has
1180 reached the last time point.
1182 .. mdp-value:: periodic
1184 The annealing will start over at the first reference point once
1185 the last reference time is reached. This is repeated until the
1188 .. mdp:: annealing-npoints
1190 A list with the number of annealing reference/control points used
1191 for each temperature group. Use 0 for groups that are not
1192 annealed. The number of entries should equal the number of
1195 .. mdp:: annealing-time
1197 List of times at the annealing reference/control points for each
1198 group. If you are using periodic annealing, the times will be used
1199 modulo the last value, *i.e.* if the values are 0, 5, 10, and 15,
1200 the coupling will restart at the 0ps value after 15ps, 30ps, 45ps,
1201 etc. The number of entries should equal the sum of the numbers
1202 given in :mdp:`annealing-npoints`.
1204 .. mdp:: annealing-temp
1206 List of temperatures at the annealing reference/control points for
1207 each group. The number of entries should equal the sum of the
1208 numbers given in :mdp:`annealing-npoints`.
1210 Confused? OK, let's use an example. Assume you have two temperature
1211 groups, set the group selections to ``annealing = single periodic``,
1212 the number of points of each group to ``annealing-npoints = 3 4``, the
1213 times to ``annealing-time = 0 3 6 0 2 4 6`` and finally temperatures
1214 to ``annealing-temp = 298 280 270 298 320 320 298``. The first group
1215 will be coupled to 298K at 0ps, but the reference temperature will
1216 drop linearly to reach 280K at 3ps, and then linearly between 280K and
1217 270K from 3ps to 6ps. After this is stays constant, at 270K. The
1218 second group is coupled to 298K at 0ps, it increases linearly to 320K
1219 at 2ps, where it stays constant until 4ps. Between 4ps and 6ps it
1220 decreases to 298K, and then it starts over with the same pattern
1221 again, *i.e.* rising linearly from 298K to 320K between 6ps and
1222 8ps. Check the summary printed by :ref:`gmx grompp` if you are unsure!
1232 Do not generate velocities. The velocities are set to zero
1233 when there are no velocities in the input structure file.
1237 Generate velocities in :ref:`gmx grompp` according to a
1238 Maxwell distribution at temperature :mdp:`gen-temp`, with
1239 random seed :mdp:`gen-seed`. This is only meaningful with
1240 :mdp-value:`integrator=md`.
1245 temperature for Maxwell distribution
1250 used to initialize random generator for random velocities,
1251 when :mdp:`gen-seed` is set to -1, a pseudo random seed is
1258 .. mdp:: constraints
1260 Controls which bonds in the topology will be converted to rigid
1261 holonomic constraints. Note that typical rigid water models do not
1262 have bonds, but rather a specialized ``[settles]`` directive, so
1263 are not affected by this keyword.
1267 No bonds converted to constraints.
1269 .. mdp-value:: h-bonds
1271 Convert the bonds with H-atoms to constraints.
1273 .. mdp-value:: all-bonds
1275 Convert all bonds to constraints.
1277 .. mdp-value:: h-angles
1279 Convert all bonds to constraints and convert the angles that
1280 involve H-atoms to bond-constraints.
1282 .. mdp-value:: all-angles
1284 Convert all bonds to constraints and all angles to bond-constraints.
1286 .. mdp:: constraint-algorithm
1288 Chooses which solver satisfies any non-SETTLE holonomic
1291 .. mdp-value:: LINCS
1293 LINear Constraint Solver. With domain decomposition the parallel
1294 version P-LINCS is used. The accuracy in set with
1295 :mdp:`lincs-order`, which sets the number of matrices in the
1296 expansion for the matrix inversion. After the matrix inversion
1297 correction the algorithm does an iterative correction to
1298 compensate for lengthening due to rotation. The number of such
1299 iterations can be controlled with :mdp:`lincs-iter`. The root
1300 mean square relative constraint deviation is printed to the log
1301 file every :mdp:`nstlog` steps. If a bond rotates more than
1302 :mdp:`lincs-warnangle` in one step, a warning will be printed
1303 both to the log file and to ``stderr``. LINCS should not be used
1304 with coupled angle constraints.
1306 .. mdp-value:: SHAKE
1308 SHAKE is slightly slower and less stable than LINCS, but does
1309 work with angle constraints. The relative tolerance is set with
1310 :mdp:`shake-tol`, 0.0001 is a good value for "normal" MD. SHAKE
1311 does not support constraints between atoms on different
1312 decomposition domains, so it can only be used with domain
1313 decomposition when so-called update-groups are used, which is
1314 usally the case when only bonds involving hydrogens are
1315 constrained. SHAKE can not be used with energy minimization.
1317 .. mdp:: continuation
1319 This option was formerly known as ``unconstrained-start``.
1323 apply constraints to the start configuration and reset shells
1327 do not apply constraints to the start configuration and do not
1328 reset shells, useful for exact coninuation and reruns
1333 relative tolerance for SHAKE
1335 .. mdp:: lincs-order
1338 Highest order in the expansion of the constraint coupling
1339 matrix. When constraints form triangles, an additional expansion of
1340 the same order is applied on top of the normal expansion only for
1341 the couplings within such triangles. For "normal" MD simulations an
1342 order of 4 usually suffices, 6 is needed for large time-steps with
1343 virtual sites or BD. For accurate energy minimization an order of 8
1344 or more might be required. With domain decomposition, the cell size
1345 is limited by the distance spanned by :mdp:`lincs-order` +1
1346 constraints. When one wants to scale further than this limit, one
1347 can decrease :mdp:`lincs-order` and increase :mdp:`lincs-iter`,
1348 since the accuracy does not deteriorate when (1+ :mdp:`lincs-iter`
1349 )* :mdp:`lincs-order` remains constant.
1354 Number of iterations to correct for rotational lengthening in
1355 LINCS. For normal runs a single step is sufficient, but for NVE
1356 runs where you want to conserve energy accurately or for accurate
1357 energy minimization you might want to increase it to 2.
1359 .. mdp:: lincs-warnangle
1362 maximum angle that a bond can rotate before LINCS will complain
1368 bonds are represented by a harmonic potential
1372 bonds are represented by a Morse potential
1375 Energy group exclusions
1376 ^^^^^^^^^^^^^^^^^^^^^^^
1378 .. mdp:: energygrp-excl
1380 Pairs of energy groups for which all non-bonded interactions are
1381 excluded. An example: if you have two energy groups ``Protein`` and
1382 ``SOL``, specifying ``energygrp-excl = Protein Protein SOL SOL``
1383 would give only the non-bonded interactions between the protein and
1384 the solvent. This is especially useful for speeding up energy
1385 calculations with ``mdrun -rerun`` and for excluding interactions
1386 within frozen groups.
1395 When set to 1 there is a wall at ``z=0``, when set to 2 there is
1396 also a wall at ``z=z-box``. Walls can only be used with :mdp:`pbc`
1397 ``=xy``. When set to 2, pressure coupling and Ewald summation can be
1398 used (it is usually best to use semiisotropic pressure coupling
1399 with the ``x/y`` compressibility set to 0, as otherwise the surface
1400 area will change). Walls interact wit the rest of the system
1401 through an optional :mdp:`wall-atomtype`. Energy groups ``wall0``
1402 and ``wall1`` (for :mdp:`nwall` =2) are added automatically to
1403 monitor the interaction of energy groups with each wall. The center
1404 of mass motion removal will be turned off in the ``z``-direction.
1406 .. mdp:: wall-atomtype
1408 the atom type name in the force field for each wall. By (for
1409 example) defining a special wall atom type in the topology with its
1410 own combination rules, this allows for independent tuning of the
1411 interaction of each atomtype with the walls.
1417 LJ integrated over the volume behind the wall: 9-3 potential
1421 LJ integrated over the wall surface: 10-4 potential
1425 direct LJ potential with the ``z`` distance from the wall
1429 user defined potentials indexed with the ``z`` distance from the
1430 wall, the tables are read analogously to the
1431 :mdp:`energygrp-table` option, where the first name is for a
1432 "normal" energy group and the second name is ``wall0`` or
1433 ``wall1``, only the dispersion and repulsion columns are used
1435 .. mdp:: wall-r-linpot
1438 Below this distance from the wall the potential is continued
1439 linearly and thus the force is constant. Setting this option to a
1440 postive value is especially useful for equilibration when some
1441 atoms are beyond a wall. When the value is <=0 (<0 for
1442 :mdp:`wall-type` =table), a fatal error is generated when atoms
1445 .. mdp:: wall-density
1447 [nm\ :sup:`-3`] / [nm\ :sup:`-2`]
1448 the number density of the atoms for each wall for wall types 9-3
1451 .. mdp:: wall-ewald-zfac
1454 The scaling factor for the third box vector for Ewald summation
1455 only, the minimum is 2. Ewald summation can only be used with
1456 :mdp:`nwall` =2, where one should use :mdp:`ewald-geometry`
1457 ``=3dc``. The empty layer in the box serves to decrease the
1458 unphysical Coulomb interaction between periodic images.
1464 Note that where pulling coordinates are applicable, there can be more
1465 than one (set with :mdp:`pull-ncoords`) and multiple related :ref:`mdp`
1466 variables will exist accordingly. Documentation references to things
1467 like :mdp:`pull-coord1-vec` should be understood to apply to to the
1468 applicable pulling coordinate, eg. the second pull coordinate is described by
1469 pull-coord2-vec, pull-coord2-k, and so on.
1475 No center of mass pulling. All the following pull options will
1476 be ignored (and if present in the :ref:`mdp` file, they unfortunately
1481 Center of mass pulling will be applied on 1 or more groups using
1482 1 or more pull coordinates.
1484 .. mdp:: pull-cylinder-r
1487 the radius of the cylinder for :mdp-value:`pull-coord1-geometry=cylinder`
1489 .. mdp:: pull-constr-tol
1492 the relative constraint tolerance for constraint pulling
1494 .. mdp:: pull-print-com
1498 do not print the COM for any group
1502 print the COM of all groups for all pull coordinates
1504 .. mdp:: pull-print-ref-value
1508 do not print the reference value for each pull coordinate
1512 print the reference value for each pull coordinate
1514 .. mdp:: pull-print-components
1518 only print the distance for each pull coordinate
1522 print the distance and Cartesian components selected in
1523 :mdp:`pull-coord1-dim`
1525 .. mdp:: pull-nstxout
1528 frequency for writing out the COMs of all the pull group (0 is
1531 .. mdp:: pull-nstfout
1534 frequency for writing out the force of all the pulled group
1537 .. mdp:: pull-pbc-ref-prev-step-com
1541 Use the reference atom (:mdp:`pull-group1-pbcatom`) for the
1542 treatment of periodic boundary conditions.
1546 Use the COM of the previous step as reference for the treatment
1547 of periodic boundary conditions. The reference is initialized
1548 using the reference atom (:mdp:`pull-group1-pbcatom`), which should
1549 be located centrally in the group. Using the COM from the
1550 previous step can be useful if one or more pull groups are large.
1552 .. mdp:: pull-xout-average
1556 Write the instantaneous coordinates for all the pulled groups.
1560 Write the average coordinates (since last output) for all the
1561 pulled groups. N.b., some analysis tools might expect instantaneous
1564 .. mdp:: pull-fout-average
1568 Write the instantaneous force for all the pulled groups.
1572 Write the average force (since last output) for all the
1573 pulled groups. N.b., some analysis tools might expect instantaneous
1576 .. mdp:: pull-ngroups
1579 The number of pull groups, not including the absolute reference
1580 group, when used. Pull groups can be reused in multiple pull
1581 coordinates. Below only the pull options for group 1 are given,
1582 further groups simply increase the group index number.
1584 .. mdp:: pull-ncoords
1587 The number of pull coordinates. Below only the pull options for
1588 coordinate 1 are given, further coordinates simply increase the
1589 coordinate index number.
1591 .. mdp:: pull-group1-name
1593 The name of the pull group, is looked up in the index file or in
1594 the default groups to obtain the atoms involved.
1596 .. mdp:: pull-group1-weights
1598 Optional relative weights which are multiplied with the masses of
1599 the atoms to give the total weight for the COM. The number should
1600 be 0, meaning all 1, or the number of atoms in the pull group.
1602 .. mdp:: pull-group1-pbcatom
1605 The reference atom for the treatment of periodic boundary
1606 conditions inside the group (this has no effect on the treatment of
1607 the pbc between groups). This option is only important when the
1608 diameter of the pull group is larger than half the shortest box
1609 vector. For determining the COM, all atoms in the group are put at
1610 their periodic image which is closest to
1611 :mdp:`pull-group1-pbcatom`. A value of 0 means that the middle
1612 atom (number wise) is used, which is only safe for small groups.
1613 :ref:`gmx grompp` checks that the maximum distance from the reference
1614 atom (specifically chosen, or not) to the other atoms in the group
1615 is not too large. This parameter is not used with
1616 :mdp:`pull-coord1-geometry` cylinder. A value of -1 turns on cosine
1617 weighting, which is useful for a group of molecules in a periodic
1618 system, *e.g.* a water slab (see Engin et al. J. Chem. Phys. B
1621 .. mdp:: pull-coord1-type
1623 .. mdp-value:: umbrella
1625 Center of mass pulling using an umbrella potential between the
1626 reference group and one or more groups.
1628 .. mdp-value:: constraint
1630 Center of mass pulling using a constraint between the reference
1631 group and one or more groups. The setup is identical to the
1632 option umbrella, except for the fact that a rigid constraint is
1633 applied instead of a harmonic potential.
1635 .. mdp-value:: constant-force
1637 Center of mass pulling using a linear potential and therefore a
1638 constant force. For this option there is no reference position
1639 and therefore the parameters :mdp:`pull-coord1-init` and
1640 :mdp:`pull-coord1-rate` are not used.
1642 .. mdp-value:: flat-bottom
1644 At distances above :mdp:`pull-coord1-init` a harmonic potential
1645 is applied, otherwise no potential is applied.
1647 .. mdp-value:: flat-bottom-high
1649 At distances below :mdp:`pull-coord1-init` a harmonic potential
1650 is applied, otherwise no potential is applied.
1652 .. mdp-value:: external-potential
1654 An external potential that needs to be provided by another
1657 .. mdp:: pull-coord1-potential-provider
1659 The name of the external module that provides the potential for
1660 the case where :mdp:`pull-coord1-type` is external-potential.
1662 .. mdp:: pull-coord1-geometry
1664 .. mdp-value:: distance
1666 Pull along the vector connecting the two groups. Components can
1667 be selected with :mdp:`pull-coord1-dim`.
1669 .. mdp-value:: direction
1671 Pull in the direction of :mdp:`pull-coord1-vec`.
1673 .. mdp-value:: direction-periodic
1675 As :mdp-value:`pull-coord1-geometry=direction`, but does not apply
1676 periodic box vector corrections to keep the distance within half
1677 the box length. This is (only) useful for pushing groups apart
1678 by more than half the box length by continuously changing the reference
1679 location using a pull rate. With this geometry the box should not be
1680 dynamic (*e.g.* no pressure scaling) in the pull dimensions and
1681 the pull force is not added to the virial.
1683 .. mdp-value:: direction-relative
1685 As :mdp-value:`pull-coord1-geometry=direction`, but the pull vector is the vector
1686 that points from the COM of a third to the COM of a fourth pull
1687 group. This means that 4 groups need to be supplied in
1688 :mdp:`pull-coord1-groups`. Note that the pull force will give
1689 rise to a torque on the pull vector, which is turn leads to
1690 forces perpendicular to the pull vector on the two groups
1691 defining the vector. If you want a pull group to move between
1692 the two groups defining the vector, simply use the union of
1693 these two groups as the reference group.
1695 .. mdp-value:: cylinder
1697 Designed for pulling with respect to a layer where the reference
1698 COM is given by a local cylindrical part of the reference group.
1699 The pulling is in the direction of :mdp:`pull-coord1-vec`. From
1700 the first of the two groups in :mdp:`pull-coord1-groups` a
1701 cylinder is selected around the axis going through the COM of
1702 the second group with direction :mdp:`pull-coord1-vec` with
1703 radius :mdp:`pull-cylinder-r`. Weights of the atoms decrease
1704 continously to zero as the radial distance goes from 0 to
1705 :mdp:`pull-cylinder-r` (mass weighting is also used). The radial
1706 dependence gives rise to radial forces on both pull groups.
1707 Note that the radius should be smaller than half the box size.
1708 For tilted cylinders they should be even smaller than half the
1709 box size since the distance of an atom in the reference group
1710 from the COM of the pull group has both a radial and an axial
1711 component. This geometry is not supported with constraint
1714 .. mdp-value:: angle
1716 Pull along an angle defined by four groups. The angle is
1717 defined as the angle between two vectors: the vector connecting
1718 the COM of the first group to the COM of the second group and
1719 the vector connecting the COM of the third group to the COM of
1722 .. mdp-value:: angle-axis
1724 As :mdp-value:`pull-coord1-geometry=angle` but the second vector is given by :mdp:`pull-coord1-vec`.
1725 Thus, only the two groups that define the first vector need to be given.
1727 .. mdp-value:: dihedral
1729 Pull along a dihedral angle defined by six groups. These pairwise
1730 define three vectors: the vector connecting the COM of group 1
1731 to the COM of group 2, the COM of group 3 to the COM of group 4,
1732 and the COM of group 5 to the COM group 6. The dihedral angle is
1733 then defined as the angle between two planes: the plane spanned by the
1734 the two first vectors and the plane spanned the two last vectors.
1737 .. mdp:: pull-coord1-groups
1739 The group indices on which this pull coordinate will operate.
1740 The number of group indices required is geometry dependent.
1741 The first index can be 0, in which case an
1742 absolute reference of :mdp:`pull-coord1-origin` is used. With an
1743 absolute reference the system is no longer translation invariant
1744 and one should think about what to do with the center of mass
1747 .. mdp:: pull-coord1-dim
1750 Selects the dimensions that this pull coordinate acts on and that
1751 are printed to the output files when
1752 :mdp:`pull-print-components` = :mdp-value:`pull-coord1-start=yes`. With
1753 :mdp:`pull-coord1-geometry` = :mdp-value:`pull-coord1-geometry=distance`, only Cartesian
1754 components set to Y contribute to the distance. Thus setting this
1755 to Y Y N results in a distance in the x/y plane. With other
1756 geometries all dimensions with non-zero entries in
1757 :mdp:`pull-coord1-vec` should be set to Y, the values for other
1758 dimensions only affect the output.
1760 .. mdp:: pull-coord1-origin
1763 The pull reference position for use with an absolute reference.
1765 .. mdp:: pull-coord1-vec
1768 The pull direction. :ref:`gmx grompp` normalizes the vector.
1770 .. mdp:: pull-coord1-start
1774 do not modify :mdp:`pull-coord1-init`
1778 add the COM distance of the starting conformation to
1779 :mdp:`pull-coord1-init`
1781 .. mdp:: pull-coord1-init
1784 The reference distance or reference angle at t=0.
1786 .. mdp:: pull-coord1-rate
1788 (0) [nm/ps] or [deg/ps]
1789 The rate of change of the reference position or reference angle.
1791 .. mdp:: pull-coord1-k
1793 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`] or
1794 [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1795 The force constant. For umbrella pulling this is the harmonic force
1796 constant in kJ mol\ :sup:`-1` nm\ :sup:`-2` (or kJ mol\ :sup:`-1` rad\ :sup:`-2`
1797 for angles). For constant force pulling this is the
1798 force constant of the linear potential, and thus the negative (!)
1799 of the constant force in kJ mol\ :sup:`-1` nm\ :sup:`-1`
1800 (or kJ mol\ :sup:`-1` rad\ :sup:`-1` for angles).
1801 Note that for angles the force constant is expressed in terms of radians
1802 (while :mdp:`pull-coord1-init` and :mdp:`pull-coord1-rate` are expressed in degrees).
1804 .. mdp:: pull-coord1-kB
1806 (pull-k1) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` nm\ :sup:`-1`]
1807 or [kJ mol\ :sup:`-1` rad\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-1`]
1808 As :mdp:`pull-coord1-k`, but for state B. This is only used when
1809 :mdp:`free-energy` is turned on. The force constant is then (1 -
1810 lambda) * :mdp:`pull-coord1-k` + lambda * :mdp:`pull-coord1-kB`.
1812 AWH adaptive biasing
1813 ^^^^^^^^^^^^^^^^^^^^
1823 Adaptively bias a reaction coordinate using the AWH method and estimate
1824 the corresponding PMF. The PMF and other AWH data are written to energy
1825 file at an interval set by :mdp:`awh-nstout` and can be extracted with
1826 the ``gmx awh`` tool. The AWH coordinate can be
1827 multidimensional and is defined by mapping each dimension to a pull coordinate index.
1828 This is only allowed if :mdp-value:`pull-coord1-type=external-potential` and
1829 :mdp:`pull-coord1-potential-provider` = ``awh`` for the concerned pull coordinate
1830 indices. Pull geometry 'direction-periodic' is not supported by AWH.
1832 .. mdp:: awh-potential
1834 .. mdp-value:: convolved
1836 The applied biasing potential is the convolution of the bias function and a
1837 set of harmonic umbrella potentials (see :mdp-value:`awh-potential=umbrella` below). This results
1838 in a smooth potential function and force. The resolution of the potential is set
1839 by the force constant of each umbrella, see :mdp:`awh1-dim1-force-constant`.
1841 .. mdp-value:: umbrella
1843 The potential bias is applied by controlling the position of an harmonic potential
1844 using Monte-Carlo sampling. The force constant is set with
1845 :mdp:`awh1-dim1-force-constant`. The umbrella location
1846 is sampled using Monte-Carlo every :mdp:`awh-nstsample` steps.
1847 There are no advantages to using an umbrella.
1848 This option is mainly for comparison and testing purposes.
1850 .. mdp:: awh-share-multisim
1854 AWH will not share biases across simulations started with
1855 :ref:`gmx mdrun` option ``-multidir``. The biases will be independent.
1859 With :ref:`gmx mdrun` and option ``-multidir`` the bias and PMF estimates
1860 for biases with :mdp:`awh1-share-group` >0 will be shared across simulations
1861 with the biases with the same :mdp:`awh1-share-group` value.
1862 The simulations should have the same AWH settings for sharing to make sense.
1863 :ref:`gmx mdrun` will check whether the simulations are technically
1864 compatible for sharing, but the user should check that bias sharing
1865 physically makes sense.
1869 (-1) Random seed for Monte-Carlo sampling the umbrella position,
1870 where -1 indicates to generate a seed. Only used with
1871 :mdp-value:`awh-potential=umbrella`.
1876 Number of steps between printing AWH data to the energy file, should be
1877 a multiple of :mdp:`nstenergy`.
1879 .. mdp:: awh-nstsample
1882 Number of steps between sampling of the coordinate value. This sampling
1883 is the basis for updating the bias and estimating the PMF and other AWH observables.
1885 .. mdp:: awh-nsamples-update
1888 The number of coordinate samples used for each AWH update.
1889 The update interval in steps is :mdp:`awh-nstsample` times this value.
1894 The number of biases, each acting on its own coordinate.
1895 The following options should be specified
1896 for each bias although below only the options for bias number 1 is shown. Options for
1897 other bias indices are obtained by replacing '1' by the bias index.
1899 .. mdp:: awh1-error-init
1901 (10.0) [kJ mol\ :sup:`-1`]
1902 Estimated initial average error of the PMF for this bias. This value together with the
1903 given diffusion constant(s) :mdp:`awh1-dim1-diffusion` determine the initial biasing rate.
1904 The error is obviously not known *a priori*. Only a rough estimate of :mdp:`awh1-error-init`
1906 As a general guideline, leave :mdp:`awh1-error-init` to its default value when starting a new
1907 simulation. On the other hand, when there is *a priori* knowledge of the PMF (e.g. when
1908 an initial PMF estimate is provided, see the :mdp:`awh1-user-data` option)
1909 then :mdp:`awh1-error-init` should reflect that knowledge.
1911 .. mdp:: awh1-growth
1913 .. mdp-value:: exp-linear
1915 Each bias keeps a reference weight histogram for the coordinate samples.
1916 Its size sets the magnitude of the bias function and free energy estimate updates
1917 (few samples corresponds to large updates and vice versa).
1918 Thus, its growth rate sets the maximum convergence rate.
1919 By default, there is an initial stage in which the histogram grows close to exponentially (but slower than the sampling rate).
1920 In the final stage that follows, the growth rate is linear and equal to the sampling rate (set by :mdp:`awh-nstsample`).
1921 The initial stage is typically necessary for efficient convergence when starting a new simulation where
1922 high free energy barriers have not yet been flattened by the bias.
1924 .. mdp-value:: linear
1926 As :mdp-value:`awh1-growth=exp-linear` but skip the initial stage. This may be useful if there is *a priori*
1927 knowledge (see :mdp:`awh1-error-init`) which eliminates the need for an initial stage. This is also
1928 the setting compatible with :mdp-value:`awh1-target=local-boltzmann`.
1930 .. mdp:: awh1-equilibrate-histogram
1934 Do not equilibrate histogram.
1938 Before entering the initial stage (see :mdp-value:`awh1-growth=exp-linear`), make sure the
1939 histogram of sampled weights is following the target distribution closely enough (specifically,
1940 at least 80% of the target region needs to have a local relative error of less than 20%). This
1941 option would typically only be used when :mdp:`awh1-share-group` > 0
1942 and the initial configurations poorly represent the target
1945 .. mdp:: awh1-target
1947 .. mdp-value:: constant
1949 The bias is tuned towards a constant (uniform) coordinate distribution
1950 in the defined sampling interval (defined by [:mdp:`awh1-dim1-start`, :mdp:`awh1-dim1-end`]).
1952 .. mdp-value:: cutoff
1954 Similar to :mdp-value:`awh1-target=constant`, but the target
1955 distribution is proportional to 1/(1 + exp(F - :mdp-value:`awh1-target=cutoff`)),
1956 where F is the free energy relative to the estimated global minimum.
1957 This provides a smooth switch of a flat target distribution in
1958 regions with free energy lower than the cut-off to a Boltzmann
1959 distribution in regions with free energy higher than the cut-off.
1961 .. mdp-value:: boltzmann
1963 The target distribution is a Boltzmann distribtution with a scaled beta (inverse temperature)
1964 factor given by :mdp:`awh1-target-beta-scaling`. *E.g.*, a value of 0.1
1965 would give the same coordinate distribution as sampling with a simulation temperature
1968 .. mdp-value:: local-boltzmann
1970 Same target distribution and use of :mdp:`awh1-target-beta-scaling`
1971 but the convergence towards the target distribution is inherently local *i.e.*, the rate of
1972 change of the bias only depends on the local sampling. This local convergence property is
1973 only compatible with :mdp-value:`awh1-growth=linear`, since for
1974 :mdp-value:`awh1-growth=exp-linear` histograms are globally rescaled in the initial stage.
1976 .. mdp:: awh1-target-beta-scaling
1979 For :mdp-value:`awh1-target=boltzmann` and :mdp-value:`awh1-target=local-boltzmann`
1980 it is the unitless beta scaling factor taking values in (0,1).
1982 .. mdp:: awh1-target-cutoff
1984 (0) [kJ mol\ :sup:`-1`]
1985 For :mdp-value:`awh1-target=cutoff` this is the cutoff, should be > 0.
1987 .. mdp:: awh1-user-data
1991 Initialize the PMF and target distribution with default values.
1995 Initialize the PMF and target distribution with user provided data. For :mdp:`awh-nbias` = 1,
1996 :ref:`gmx mdrun` will expect a file ``awhinit.xvg`` to be present in the run directory.
1997 For multiple biases, :ref:`gmx mdrun` expects files ``awhinit1.xvg``, ``awhinit2.xvg``, etc.
1998 The file name can be changed with the ``-awh`` option.
1999 The first :mdp:`awh1-ndim` columns of
2000 each input file should contain the coordinate values, such that each row defines a point in
2001 coordinate space. Column :mdp:`awh1-ndim` + 1 should contain the PMF value for each point.
2002 The target distribution column can either follow the PMF (column :mdp:`awh1-ndim` + 2) or
2003 be in the same column as written by :ref:`gmx awh`.
2005 .. mdp:: awh1-share-group
2009 Do not share the bias.
2011 .. mdp-value:: positive
2013 Share the bias and PMF estimates within and/or between simulations.
2014 Within a simulation, the bias will be shared between biases that have the
2015 same :mdp:`awh1-share-group` index (note that the current code does not support this).
2016 With :mdp-value:`awh-share-multisim=yes` and
2017 :ref:`gmx mdrun` option ``-multidir`` the bias will also be shared across simulations.
2018 Sharing may increase convergence initially, although the starting configurations
2019 can be critical, especially when sharing between many biases.
2020 Currently, positive group values should start at 1 and increase
2021 by 1 for each subsequent bias that is shared.
2026 Number of dimensions of the coordinate, each dimension maps to 1 pull coordinate.
2027 The following options should be specified for each such dimension. Below only
2028 the options for dimension number 1 is shown. Options for other dimension indices are
2029 obtained by replacing '1' by the dimension index.
2031 .. mdp:: awh1-dim1-coord-provider
2035 The module providing the reaction coordinate for this dimension.
2036 Currently AWH can only act on pull coordinates.
2038 .. mdp:: awh1-dim1-coord-index
2041 Index of the pull coordinate defining this coordinate dimension.
2043 .. mdp:: awh1-dim1-force-constant
2045 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`] or [kJ mol\ :sup:`-1` rad\ :sup:`-2`]
2046 Force constant for the (convolved) umbrella potential(s) along this
2047 coordinate dimension.
2049 .. mdp:: awh1-dim1-start
2052 Start value of the sampling interval along this dimension. The range of allowed
2053 values depends on the relevant pull geometry (see :mdp:`pull-coord1-geometry`).
2054 For dihedral geometries :mdp:`awh1-dim1-start` greater than :mdp:`awh1-dim1-end`
2055 is allowed. The interval will then wrap around from +period/2 to -period/2.
2056 For the direction geometry, the dimension is made periodic when
2057 the direction is along a box vector and covers more than 95%
2058 of the box length. Note that one should not apply pressure coupling
2059 along a periodic dimension.
2061 .. mdp:: awh1-dim1-end
2064 End value defining the sampling interval together with :mdp:`awh1-dim1-start`.
2066 .. mdp:: awh1-dim1-diffusion
2068 (10\ :sup:`-5`) [nm\ :sup:`2`/ps] or [rad\ :sup:`2`/ps]
2069 Estimated diffusion constant for this coordinate dimension determining the initial
2070 biasing rate. This needs only be a rough estimate and should not critically
2071 affect the results unless it is set to something very low, leading to slow convergence,
2072 or very high, forcing the system far from equilibrium. Not setting this value
2073 explicitly generates a warning.
2075 .. mdp:: awh1-dim1-cover-diameter
2078 Diameter that needs to be sampled by a single simulation around a coordinate value
2079 before the point is considered covered in the initial stage (see :mdp-value:`awh1-growth=exp-linear`).
2080 A value > 0 ensures that for each covering there is a continuous transition of this diameter
2081 across each coordinate value.
2082 This is trivially true for independent simulations but not for for multiple bias-sharing simulations
2083 (:mdp:`awh1-share-group`>0).
2084 For a diameter = 0, covering occurs as soon as the simulations have sampled the whole interval, which
2085 for many sharing simulations does not guarantee transitions across free energy barriers.
2086 On the other hand, when the diameter >= the sampling interval length, covering occurs when a single simulation
2087 has independently sampled the whole interval.
2092 These :ref:`mdp` parameters can be used enforce the rotation of a group of atoms,
2093 e.g. a protein subunit. The `reference manual`_ describes in detail 13 different potentials
2094 that can be used to achieve such a rotation.
2100 No enforced rotation will be applied. All enforced rotation options will
2101 be ignored (and if present in the :ref:`mdp` file, they unfortunately
2106 Apply the rotation potential specified by :mdp:`rot-type0` to the group of atoms given
2107 under the :mdp:`rot-group0` option.
2109 .. mdp:: rot-ngroups
2112 Number of rotation groups.
2116 Name of rotation group 0 in the index file.
2121 Type of rotation potential that is applied to rotation group 0. Can be of of the following:
2122 ``iso``, ``iso-pf``, ``pm``, ``pm-pf``, ``rm``, ``rm-pf``, ``rm2``, ``rm2-pf``,
2123 ``flex``, ``flex-t``, ``flex2``, or ``flex2-t``.
2128 Use mass weighted rotation group positions.
2133 Rotation vector, will get normalized.
2138 Pivot point for the potentials ``iso``, ``pm``, ``rm``, and ``rm2``.
2142 (0) [degree ps\ :sup:`-1`]
2143 Reference rotation rate of group 0.
2147 (0) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2148 Force constant for group 0.
2150 .. mdp:: rot-slab-dist0
2153 Slab distance, if a flexible axis rotation type was chosen.
2155 .. mdp:: rot-min-gauss0
2158 Minimum value (cutoff) of Gaussian function for the force to be evaluated
2159 (for the flexible axis potentials).
2163 (0.0001) [nm\ :sup:`2`]
2164 Value of additive constant epsilon for ``rm2*`` and ``flex2*`` potentials.
2166 .. mdp:: rot-fit-method0
2169 Fitting method when determining the actual angle of a rotation group
2170 (can be one of ``rmsd``, ``norm``, or ``potential``).
2172 .. mdp:: rot-potfit-nsteps0
2175 For fit type ``potential``, the number of angular positions around the reference angle for which the
2176 rotation potential is evaluated.
2178 .. mdp:: rot-potfit-step0
2181 For fit type ``potential``, the distance in degrees between two angular positions.
2183 .. mdp:: rot-nstrout
2186 Output frequency (in steps) for the angle of the rotation group, as well as for the torque
2187 and the rotation potential energy.
2189 .. mdp:: rot-nstsout
2192 Output frequency for per-slab data of the flexible axis potentials, i.e. angles, torques and slab centers.
2202 ignore distance restraint information in topology file
2204 .. mdp-value:: simple
2206 simple (per-molecule) distance restraints.
2208 .. mdp-value:: ensemble
2210 distance restraints over an ensemble of molecules in one
2211 simulation box. Normally, one would perform ensemble averaging
2212 over multiple simulations, using ``mdrun
2213 -multidir``. The environment
2214 variable ``GMX_DISRE_ENSEMBLE_SIZE`` sets the number of systems
2215 within each ensemble (usually equal to the number of directories
2216 supplied to ``mdrun -multidir``).
2218 .. mdp:: disre-weighting
2220 .. mdp-value:: equal
2222 divide the restraint force equally over all atom pairs in the
2225 .. mdp-value:: conservative
2227 the forces are the derivative of the restraint potential, this
2228 results in an weighting of the atom pairs to the reciprocal
2229 seventh power of the displacement. The forces are conservative
2230 when :mdp:`disre-tau` is zero.
2232 .. mdp:: disre-mixed
2236 the violation used in the calculation of the restraint force is
2237 the time-averaged violation
2241 the violation used in the calculation of the restraint force is
2242 the square root of the product of the time-averaged violation
2243 and the instantaneous violation
2247 (1000) [kJ mol\ :sup:`-1` nm\ :sup:`-2`]
2248 force constant for distance restraints, which is multiplied by a
2249 (possibly) different factor for each restraint given in the `fac`
2250 column of the interaction in the topology file.
2255 time constant for distance restraints running average. A value of
2256 zero turns off time averaging.
2258 .. mdp:: nstdisreout
2261 period between steps when the running time-averaged and
2262 instantaneous distances of all atom pairs involved in restraints
2263 are written to the energy file (can make the energy file very
2270 ignore orientation restraint information in topology file
2274 use orientation restraints, ensemble averaging can be performed
2275 with ``mdrun -multidir``
2279 (0) [kJ mol\ :sup:`-1`]
2280 force constant for orientation restraints, which is multiplied by a
2281 (possibly) different weight factor for each restraint, can be set
2282 to zero to obtain the orientations from a free simulation
2287 time constant for orientation restraints running average. A value
2288 of zero turns off time averaging.
2290 .. mdp:: orire-fitgrp
2292 fit group for orientation restraining. This group of atoms is used
2293 to determine the rotation **R** of the system with respect to the
2294 reference orientation. The reference orientation is the starting
2295 conformation of the first subsystem. For a protein, backbone is a
2298 .. mdp:: nstorireout
2301 period between steps when the running time-averaged and
2302 instantaneous orientations for all restraints, and the molecular
2303 order tensor are written to the energy file (can make the energy
2307 Free energy calculations
2308 ^^^^^^^^^^^^^^^^^^^^^^^^
2310 .. mdp:: free-energy
2314 Only use topology A.
2318 Interpolate between topology A (lambda=0) to topology B
2319 (lambda=1) and write the derivative of the Hamiltonian with
2320 respect to lambda (as specified with :mdp:`dhdl-derivatives`),
2321 or the Hamiltonian differences with respect to other lambda
2322 values (as specified with foreign lambda) to the energy file
2323 and/or to ``dhdl.xvg``, where they can be processed by, for
2324 example :ref:`gmx bar`. The potentials, bond-lengths and angles
2325 are interpolated linearly as described in the manual. When
2326 :mdp:`sc-alpha` is larger than zero, soft-core potentials are
2327 used for the LJ and Coulomb interactions.
2331 Turns on expanded ensemble simulation, where the alchemical state
2332 becomes a dynamic variable, allowing jumping between different
2333 Hamiltonians. See the expanded ensemble options for controlling how
2334 expanded ensemble simulations are performed. The different
2335 Hamiltonians used in expanded ensemble simulations are defined by
2336 the other free energy options.
2338 .. mdp:: init-lambda
2341 starting value for lambda (float). Generally, this should only be
2342 used with slow growth (*i.e.* nonzero :mdp:`delta-lambda`). In
2343 other cases, :mdp:`init-lambda-state` should be specified
2344 instead. Must be greater than or equal to 0.
2346 .. mdp:: delta-lambda
2349 increment per time step for lambda
2351 .. mdp:: init-lambda-state
2354 starting value for the lambda state (integer). Specifies which
2355 columm of the lambda vector (:mdp:`coul-lambdas`,
2356 :mdp:`vdw-lambdas`, :mdp:`bonded-lambdas`,
2357 :mdp:`restraint-lambdas`, :mdp:`mass-lambdas`,
2358 :mdp:`temperature-lambdas`, :mdp:`fep-lambdas`) should be
2359 used. This is a zero-based index: :mdp:`init-lambda-state` 0 means
2360 the first column, and so on.
2362 .. mdp:: fep-lambdas
2365 Zero, one or more lambda values for which Delta H values will be
2366 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2367 steps. Values must be between 0 and 1. Free energy differences
2368 between different lambda values can then be determined with
2369 :ref:`gmx bar`. :mdp:`fep-lambdas` is different from the
2370 other -lambdas keywords because all components of the lambda vector
2371 that are not specified will use :mdp:`fep-lambdas` (including
2372 :mdp:`restraint-lambdas` and therefore the pull code restraints).
2374 .. mdp:: coul-lambdas
2377 Zero, one or more lambda values for which Delta H values will be
2378 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2379 steps. Values must be between 0 and 1. Only the electrostatic
2380 interactions are controlled with this component of the lambda
2381 vector (and only if the lambda=0 and lambda=1 states have differing
2382 electrostatic interactions).
2384 .. mdp:: vdw-lambdas
2387 Zero, one or more lambda values for which Delta H values will be
2388 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2389 steps. Values must be between 0 and 1. Only the van der Waals
2390 interactions are controlled with this component of the lambda
2393 .. mdp:: bonded-lambdas
2396 Zero, one or more lambda values for which Delta H values will be
2397 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2398 steps. Values must be between 0 and 1. Only the bonded interactions
2399 are controlled with this component of the lambda vector.
2401 .. mdp:: restraint-lambdas
2404 Zero, one or more lambda values for which Delta H values will be
2405 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2406 steps. Values must be between 0 and 1. Only the restraint
2407 interactions: dihedral restraints, and the pull code restraints are
2408 controlled with this component of the lambda vector.
2410 .. mdp:: mass-lambdas
2413 Zero, one or more lambda values for which Delta H values will be
2414 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2415 steps. Values must be between 0 and 1. Only the particle masses are
2416 controlled with this component of the lambda vector.
2418 .. mdp:: temperature-lambdas
2421 Zero, one or more lambda values for which Delta H values will be
2422 determined and written to dhdl.xvg every :mdp:`nstdhdl`
2423 steps. Values must be between 0 and 1. Only the temperatures
2424 controlled with this component of the lambda vector. Note that
2425 these lambdas should not be used for replica exchange, only for
2426 simulated tempering.
2428 .. mdp:: calc-lambda-neighbors
2431 Controls the number of lambda values for which Delta H values will
2432 be calculated and written out, if :mdp:`init-lambda-state` has
2433 been set. A positive value will limit the number of lambda points
2434 calculated to only the nth neighbors of :mdp:`init-lambda-state`:
2435 for example, if :mdp:`init-lambda-state` is 5 and this parameter
2436 has a value of 2, energies for lambda points 3-7 will be calculated
2437 and writen out. A value of -1 means all lambda points will be
2438 written out. For normal BAR such as with :ref:`gmx bar`, a value of
2439 1 is sufficient, while for MBAR -1 should be used.
2444 the soft-core alpha parameter, a value of 0 results in linear
2445 interpolation of the LJ and Coulomb interactions
2450 power 6 for the radial term in the soft-core equation.
2453 (deprecated) power 48 for the radial term in the soft-core equation.
2454 Note that sc-alpha should generally be much lower (between 0.001 and 0.003).
2459 Whether to apply the soft-core free energy interaction
2460 transformation to the Columbic interaction of a molecule. Default
2461 is no, as it is generally more efficient to turn off the Coulomic
2462 interactions linearly before turning off the van der Waals
2463 interactions. Note that it is only taken into account when lambda
2464 states are used, not with :mdp:`couple-lambda0` /
2465 :mdp:`couple-lambda1`, and you can still turn off soft-core
2466 interactions by setting :mdp:`sc-alpha` to 0.
2471 the power for lambda in the soft-core function, only the values 1
2477 the soft-core sigma for particles which have a C6 or C12 parameter
2478 equal to zero or a sigma smaller than :mdp:`sc-sigma`
2480 .. mdp:: couple-moltype
2482 Here one can supply a molecule type (as defined in the topology)
2483 for calculating solvation or coupling free energies. There is a
2484 special option ``system`` that couples all molecule types in the
2485 system. This can be useful for equilibrating a system starting from
2486 (nearly) random coordinates. :mdp:`free-energy` has to be turned
2487 on. The Van der Waals interactions and/or charges in this molecule
2488 type can be turned on or off between lambda=0 and lambda=1,
2489 depending on the settings of :mdp:`couple-lambda0` and
2490 :mdp:`couple-lambda1`. If you want to decouple one of several
2491 copies of a molecule, you need to copy and rename the molecule
2492 definition in the topology.
2494 .. mdp:: couple-lambda0
2496 .. mdp-value:: vdw-q
2498 all interactions are on at lambda=0
2502 the charges are zero (no Coulomb interactions) at lambda=0
2506 the Van der Waals interactions are turned at lambda=0; soft-core
2507 interactions will be required to avoid singularities
2511 the Van der Waals interactions are turned off and the charges
2512 are zero at lambda=0; soft-core interactions will be required to
2513 avoid singularities.
2515 .. mdp:: couple-lambda1
2517 analogous to :mdp:`couple-lambda1`, but for lambda=1
2519 .. mdp:: couple-intramol
2523 All intra-molecular non-bonded interactions for moleculetype
2524 :mdp:`couple-moltype` are replaced by exclusions and explicit
2525 pair interactions. In this manner the decoupled state of the
2526 molecule corresponds to the proper vacuum state without
2527 periodicity effects.
2531 The intra-molecular Van der Waals and Coulomb interactions are
2532 also turned on/off. This can be useful for partitioning
2533 free-energies of relatively large molecules, where the
2534 intra-molecular non-bonded interactions might lead to
2535 kinetically trapped vacuum conformations. The 1-4 pair
2536 interactions are not turned off.
2541 the frequency for writing dH/dlambda and possibly Delta H to
2542 dhdl.xvg, 0 means no ouput, should be a multiple of
2543 :mdp:`nstcalcenergy`.
2545 .. mdp:: dhdl-derivatives
2549 If yes (the default), the derivatives of the Hamiltonian with
2550 respect to lambda at each :mdp:`nstdhdl` step are written
2551 out. These values are needed for interpolation of linear energy
2552 differences with :ref:`gmx bar` (although the same can also be
2553 achieved with the right foreign lambda setting, that may not be as
2554 flexible), or with thermodynamic integration
2556 .. mdp:: dhdl-print-energy
2560 Include either the total or the potential energy in the dhdl
2561 file. Options are 'no', 'potential', or 'total'. This information
2562 is needed for later free energy analysis if the states of interest
2563 are at different temperatures. If all states are at the same
2564 temperature, this information is not needed. 'potential' is useful
2565 in case one is using ``mdrun -rerun`` to generate the ``dhdl.xvg``
2566 file. When rerunning from an existing trajectory, the kinetic
2567 energy will often not be correct, and thus one must compute the
2568 residual free energy from the potential alone, with the kinetic
2569 energy component computed analytically.
2571 .. mdp:: separate-dhdl-file
2575 The free energy values that are calculated (as specified with
2576 the foreign lambda and :mdp:`dhdl-derivatives` settings) are
2577 written out to a separate file, with the default name
2578 ``dhdl.xvg``. This file can be used directly with :ref:`gmx
2583 The free energy values are written out to the energy output file
2584 (``ener.edr``, in accumulated blocks at every :mdp:`nstenergy`
2585 steps), where they can be extracted with :ref:`gmx energy` or
2586 used directly with :ref:`gmx bar`.
2588 .. mdp:: dh-hist-size
2591 If nonzero, specifies the size of the histogram into which the
2592 Delta H values (specified with foreign lambda) and the derivative
2593 dH/dl values are binned, and written to ener.edr. This can be used
2594 to save disk space while calculating free energy differences. One
2595 histogram gets written for each foreign lambda and two for the
2596 dH/dl, at every :mdp:`nstenergy` step. Be aware that incorrect
2597 histogram settings (too small size or too wide bins) can introduce
2598 errors. Do not use histograms unless you're certain you need it.
2600 .. mdp:: dh-hist-spacing
2603 Specifies the bin width of the histograms, in energy units. Used in
2604 conjunction with :mdp:`dh-hist-size`. This size limits the
2605 accuracy with which free energies can be calculated. Do not use
2606 histograms unless you're certain you need it.
2609 Expanded Ensemble calculations
2610 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2612 .. mdp:: nstexpanded
2614 The number of integration steps beween attempted moves changing the
2615 system Hamiltonian in expanded ensemble simulations. Must be a
2616 multiple of :mdp:`nstcalcenergy`, but can be greater or less than
2623 No Monte Carlo in state space is performed.
2625 .. mdp-value:: metropolis-transition
2627 Uses the Metropolis weights to update the expanded ensemble
2628 weight of each state. Min{1,exp(-(beta_new u_new - beta_old
2631 .. mdp-value:: barker-transition
2633 Uses the Barker transition critera to update the expanded
2634 ensemble weight of each state i, defined by exp(-beta_new
2635 u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2637 .. mdp-value:: wang-landau
2639 Uses the Wang-Landau algorithm (in state space, not energy
2640 space) to update the expanded ensemble weights.
2642 .. mdp-value:: min-variance
2644 Uses the minimum variance updating method of Escobedo et al. to
2645 update the expanded ensemble weights. Weights will not be the
2646 free energies, but will rather emphasize states that need more
2647 sampling to give even uncertainty.
2649 .. mdp:: lmc-mc-move
2653 No Monte Carlo in state space is performed.
2655 .. mdp-value:: metropolis-transition
2657 Randomly chooses a new state up or down, then uses the
2658 Metropolis critera to decide whether to accept or reject:
2659 Min{1,exp(-(beta_new u_new - beta_old u_old)}
2661 .. mdp-value:: barker-transition
2663 Randomly chooses a new state up or down, then uses the Barker
2664 transition critera to decide whether to accept or reject:
2665 exp(-beta_new u_new)/(exp(-beta_new u_new)+exp(-beta_old u_old))
2667 .. mdp-value:: gibbs
2669 Uses the conditional weights of the state given the coordinate
2670 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2673 .. mdp-value:: metropolized-gibbs
2675 Uses the conditional weights of the state given the coordinate
2676 (exp(-beta_i u_i) / sum_k exp(beta_i u_i) to decide which state
2677 to move to, EXCLUDING the current state, then uses a rejection
2678 step to ensure detailed balance. Always more efficient that
2679 Gibbs, though only marginally so in many situations, such as
2680 when only the nearest neighbors have decent phase space
2686 random seed to use for Monte Carlo moves in state space. When
2687 :mdp:`lmc-seed` is set to -1, a pseudo random seed is us
2689 .. mdp:: mc-temperature
2691 Temperature used for acceptance/rejection for Monte Carlo moves. If
2692 not specified, the temperature of the simulation specified in the
2693 first group of :mdp:`ref-t` is used.
2698 The cutoff for the histogram of state occupancies to be reset, and
2699 the free energy incrementor to be changed from delta to delta *
2700 :mdp:`wl-scale`. If we define the Nratio = (number of samples at
2701 each histogram) / (average number of samples at each
2702 histogram). :mdp:`wl-ratio` of 0.8 means that means that the
2703 histogram is only considered flat if all Nratio > 0.8 AND
2704 simultaneously all 1/Nratio > 0.8.
2709 Each time the histogram is considered flat, then the current value
2710 of the Wang-Landau incrementor for the free energies is multiplied
2711 by :mdp:`wl-scale`. Value must be between 0 and 1.
2713 .. mdp:: init-wl-delta
2716 The initial value of the Wang-Landau incrementor in kT. Some value
2717 near 1 kT is usually most efficient, though sometimes a value of
2718 2-3 in units of kT works better if the free energy differences are
2721 .. mdp:: wl-oneovert
2724 Set Wang-Landau incrementor to scale with 1/(simulation time) in
2725 the large sample limit. There is significant evidence that the
2726 standard Wang-Landau algorithms in state space presented here
2727 result in free energies getting 'burned in' to incorrect values
2728 that depend on the initial state. when :mdp:`wl-oneovert` is true,
2729 then when the incrementor becomes less than 1/N, where N is the
2730 mumber of samples collected (and thus proportional to the data
2731 collection time, hence '1 over t'), then the Wang-Lambda
2732 incrementor is set to 1/N, decreasing every step. Once this occurs,
2733 :mdp:`wl-ratio` is ignored, but the weights will still stop
2734 updating when the equilibration criteria set in
2735 :mdp:`lmc-weights-equil` is achieved.
2737 .. mdp:: lmc-repeats
2740 Controls the number of times that each Monte Carlo swap type is
2741 performed each iteration. In the limit of large numbers of Monte
2742 Carlo repeats, then all methods converge to Gibbs sampling. The
2743 value will generally not need to be different from 1.
2745 .. mdp:: lmc-gibbsdelta
2748 Limit Gibbs sampling to selected numbers of neighboring states. For
2749 Gibbs sampling, it is sometimes inefficient to perform Gibbs
2750 sampling over all of the states that are defined. A positive value
2751 of :mdp:`lmc-gibbsdelta` means that only states plus or minus
2752 :mdp:`lmc-gibbsdelta` are considered in exchanges up and down. A
2753 value of -1 means that all states are considered. For less than 100
2754 states, it is probably not that expensive to include all states.
2756 .. mdp:: lmc-forced-nstart
2759 Force initial state space sampling to generate weights. In order to
2760 come up with reasonable initial weights, this setting allows the
2761 simulation to drive from the initial to the final lambda state,
2762 with :mdp:`lmc-forced-nstart` steps at each state before moving on
2763 to the next lambda state. If :mdp:`lmc-forced-nstart` is
2764 sufficiently long (thousands of steps, perhaps), then the weights
2765 will be close to correct. However, in most cases, it is probably
2766 better to simply run the standard weight equilibration algorithms.
2768 .. mdp:: nst-transition-matrix
2771 Frequency of outputting the expanded ensemble transition matrix. A
2772 negative number means it will only be printed at the end of the
2775 .. mdp:: symmetrized-transition-matrix
2778 Whether to symmetrize the empirical transition matrix. In the
2779 infinite limit the matrix will be symmetric, but will diverge with
2780 statistical noise for short timescales. Forced symmetrization, by
2781 using the matrix T_sym = 1/2 (T + transpose(T)), removes problems
2782 like the existence of (small magnitude) negative eigenvalues.
2784 .. mdp:: mininum-var-min
2787 The min-variance strategy (option of :mdp:`lmc-stats` is only
2788 valid for larger number of samples, and can get stuck if too few
2789 samples are used at each state. :mdp:`mininum-var-min` is the
2790 minimum number of samples that each state that are allowed before
2791 the min-variance strategy is activated if selected.
2793 .. mdp:: init-lambda-weights
2795 The initial weights (free energies) used for the expanded ensemble
2796 states. Default is a vector of zero weights. format is similar to
2797 the lambda vector settings in :mdp:`fep-lambdas`, except the
2798 weights can be any floating point number. Units are kT. Its length
2799 must match the lambda vector lengths.
2801 .. mdp:: lmc-weights-equil
2805 Expanded ensemble weights continue to be updated throughout the
2810 The input expanded ensemble weights are treated as equilibrated,
2811 and are not updated throughout the simulation.
2813 .. mdp-value:: wl-delta
2815 Expanded ensemble weight updating is stopped when the
2816 Wang-Landau incrementor falls below this value.
2818 .. mdp-value:: number-all-lambda
2820 Expanded ensemble weight updating is stopped when the number of
2821 samples at all of the lambda states is greater than this value.
2823 .. mdp-value:: number-steps
2825 Expanded ensemble weight updating is stopped when the number of
2826 steps is greater than the level specified by this value.
2828 .. mdp-value:: number-samples
2830 Expanded ensemble weight updating is stopped when the number of
2831 total samples across all lambda states is greater than the level
2832 specified by this value.
2834 .. mdp-value:: count-ratio
2836 Expanded ensemble weight updating is stopped when the ratio of
2837 samples at the least sampled lambda state and most sampled
2838 lambda state greater than this value.
2840 .. mdp:: simulated-tempering
2843 Turn simulated tempering on or off. Simulated tempering is
2844 implemented as expanded ensemble sampling with different
2845 temperatures instead of different Hamiltonians.
2847 .. mdp:: sim-temp-low
2850 Low temperature for simulated tempering.
2852 .. mdp:: sim-temp-high
2855 High temperature for simulated tempering.
2857 .. mdp:: simulated-tempering-scaling
2859 Controls the way that the temperatures at intermediate lambdas are
2860 calculated from the :mdp:`temperature-lambdas` part of the lambda
2863 .. mdp-value:: linear
2865 Linearly interpolates the temperatures using the values of
2866 :mdp:`temperature-lambdas`, *i.e.* if :mdp:`sim-temp-low`
2867 =300, :mdp:`sim-temp-high` =400, then lambda=0.5 correspond to
2868 a temperature of 350. A nonlinear set of temperatures can always
2869 be implemented with uneven spacing in lambda.
2871 .. mdp-value:: geometric
2873 Interpolates temperatures geometrically between
2874 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2875 has temperature :mdp:`sim-temp-low` * (:mdp:`sim-temp-high` /
2876 :mdp:`sim-temp-low`) raised to the power of
2877 (i/(ntemps-1)). This should give roughly equal exchange for
2878 constant heat capacity, though of course things simulations that
2879 involve protein folding have very high heat capacity peaks.
2881 .. mdp-value:: exponential
2883 Interpolates temperatures exponentially between
2884 :mdp:`sim-temp-low` and :mdp:`sim-temp-high`. The i:th state
2885 has temperature :mdp:`sim-temp-low` + (:mdp:`sim-temp-high` -
2886 :mdp:`sim-temp-low`)*((exp(:mdp:`temperature-lambdas`
2887 (i))-1)/(exp(1.0)-i)).
2895 groups for constant acceleration (*e.g.* ``Protein Sol``) all atoms
2896 in groups Protein and Sol will experience constant acceleration as
2897 specified in the :mdp:`accelerate` line
2901 (0) [nm ps\ :sup:`-2`]
2902 acceleration for :mdp:`acc-grps`; x, y and z for each group
2903 (*e.g.* ``0.1 0.0 0.0 -0.1 0.0 0.0`` means that first group has
2904 constant acceleration of 0.1 nm ps\ :sup:`-2` in X direction, second group
2909 Groups that are to be frozen (*i.e.* their X, Y, and/or Z position
2910 will not be updated; *e.g.* ``Lipid SOL``). :mdp:`freezedim`
2911 specifies for which dimension(s) the freezing applies. To avoid
2912 spurious contributions to the virial and pressure due to large
2913 forces between completely frozen atoms you need to use energy group
2914 exclusions, this also saves computing time. Note that coordinates
2915 of frozen atoms are not scaled by pressure-coupling algorithms.
2919 dimensions for which groups in :mdp:`freezegrps` should be frozen,
2920 specify `Y` or `N` for X, Y and Z and for each group (*e.g.* ``Y Y
2921 N N N N`` means that particles in the first group can move only in
2922 Z direction. The particles in the second group can move in any
2925 .. mdp:: cos-acceleration
2927 (0) [nm ps\ :sup:`-2`]
2928 the amplitude of the acceleration profile for calculating the
2929 viscosity. The acceleration is in the X-direction and the magnitude
2930 is :mdp:`cos-acceleration` cos(2 pi z/boxheight). Two terms are
2931 added to the energy file: the amplitude of the velocity profile and
2936 (0 0 0 0 0 0) [nm ps\ :sup:`-1`]
2937 The velocities of deformation for the box elements: a(x) b(y) c(z)
2938 b(x) c(x) c(y). Each step the box elements for which :mdp:`deform`
2939 is non-zero are calculated as: box(ts)+(t-ts)*deform, off-diagonal
2940 elements are corrected for periodicity. The coordinates are
2941 transformed accordingly. Frozen degrees of freedom are (purposely)
2942 also transformed. The time ts is set to t at the first step and at
2943 steps at which x and v are written to trajectory to ensure exact
2944 restarts. Deformation can be used together with semiisotropic or
2945 anisotropic pressure coupling when the appropriate
2946 compressibilities are set to zero. The diagonal elements can be
2947 used to strain a solid. The off-diagonal elements can be used to
2948 shear a solid or a liquid.
2954 .. mdp:: electric-field-x
2955 .. mdp:: electric-field-y
2956 .. mdp:: electric-field-z
2958 Here you can specify an electric field that optionally can be
2959 alternating and pulsed. The general expression for the field
2960 has the form of a gaussian laser pulse:
2962 .. math:: E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
2964 For example, the four parameters for direction x are set in the
2965 fields of :mdp:`electric-field-x` (and similar for ``electric-field-y``
2966 and ``electric-field-z``) like
2968 ``electric-field-x = E0 omega t0 sigma``
2970 with units (respectively) V nm\ :sup:`-1`, ps\ :sup:`-1`, ps, ps.
2972 In the special case that ``sigma = 0``, the exponential term is omitted
2973 and only the cosine term is used. If also ``omega = 0`` a static
2974 electric field is applied.
2976 Read more at :ref:`electric fields` and in ref. \ :ref:`146 <refCaleman2008a>`.
2979 Mixed quantum/classical molecular dynamics
2980 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2990 Do a QM/MM simulation. Several groups can be described at
2991 different QM levels separately. These are specified in the
2992 :mdp:`QMMM-grps` field separated by spaces. The level of *ab
2993 initio* theory at which the groups are described is specified by
2994 :mdp:`QMmethod` and :mdp:`QMbasis` Fields. Describing the
2995 groups at different levels of theory is only possible with the
2996 ONIOM QM/MM scheme, specified by :mdp:`QMMMscheme`.
3000 groups to be descibed at the QM level (works also in case of MiMiC QM/MM)
3004 .. mdp-value:: normal
3006 normal QM/MM. There can only be one :mdp:`QMMM-grps` that is
3007 modelled at the :mdp:`QMmethod` and :mdp:`QMbasis` level of
3008 *ab initio* theory. The rest of the system is described at the
3009 MM level. The QM and MM subsystems interact as follows: MM point
3010 charges are included in the QM one-electron hamiltonian and all
3011 Lennard-Jones interactions are described at the MM level.
3013 .. mdp-value:: ONIOM
3015 The interaction between the subsystem is described using the
3016 ONIOM method by Morokuma and co-workers. There can be more than
3017 one :mdp:`QMMM-grps` each modeled at a different level of QM
3018 theory (:mdp:`QMmethod` and :mdp:`QMbasis`).
3023 Method used to compute the energy and gradients on the QM
3024 atoms. Available methods are AM1, PM3, RHF, UHF, DFT, B3LYP, MP2,
3025 CASSCF, and MMVB. For CASSCF, the number of electrons and orbitals
3026 included in the active space is specified by :mdp:`CASelectrons`
3027 and :mdp:`CASorbitals`.
3032 Basis set used to expand the electronic wavefuntion. Only Gaussian
3033 basis sets are currently available, *i.e.* ``STO-3G, 3-21G, 3-21G*,
3034 3-21+G*, 6-21G, 6-31G, 6-31G*, 6-31+G*,`` and ``6-311G``.
3039 The total charge in `e` of the :mdp:`QMMM-grps`. In case there are
3040 more than one :mdp:`QMMM-grps`, the total charge of each ONIOM
3041 layer needs to be specified separately.
3046 The multiplicity of the :mdp:`QMMM-grps`. In case there are more
3047 than one :mdp:`QMMM-grps`, the multiplicity of each ONIOM layer
3048 needs to be specified separately.
3050 .. mdp:: CASorbitals
3053 The number of orbitals to be included in the active space when
3054 doing a CASSCF computation.
3056 .. mdp:: CASelectrons
3059 The number of electrons to be included in the active space when
3060 doing a CASSCF computation.
3066 No surface hopping. The system is always in the electronic
3071 Do a QM/MM MD simulation on the excited state-potential energy
3072 surface and enforce a *diabatic* hop to the ground-state when
3073 the system hits the conical intersection hyperline in the course
3074 the simulation. This option only works in combination with the
3078 Computational Electrophysiology
3079 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
3080 Use these options to switch on and control ion/water position exchanges in "Computational
3081 Electrophysiology" simulation setups. (See the `reference manual`_ for details).
3087 Do not enable ion/water position exchanges.
3089 .. mdp-value:: X ; Y ; Z
3091 Allow for ion/water position exchanges along the chosen direction.
3092 In a typical setup with the membranes parallel to the x-y plane,
3093 ion/water pairs need to be exchanged in Z direction to sustain the
3094 requested ion concentrations in the compartments.
3096 .. mdp:: swap-frequency
3098 (1) The swap attempt frequency, i.e. every how many time steps the ion counts
3099 per compartment are determined and exchanges made if necessary.
3100 Normally it is not necessary to check at every time step.
3101 For typical Computational Electrophysiology setups, a value of about 100 is
3102 sufficient and yields a negligible performance impact.
3104 .. mdp:: split-group0
3106 Name of the index group of the membrane-embedded part of channel #0.
3107 The center of mass of these atoms defines one of the compartment boundaries
3108 and should be chosen such that it is near the center of the membrane.
3110 .. mdp:: split-group1
3112 Channel #1 defines the position of the other compartment boundary.
3114 .. mdp:: massw-split0
3116 (no) Defines whether or not mass-weighting is used to calculate the split group center.
3120 Use the geometrical center.
3124 Use the center of mass.
3126 .. mdp:: massw-split1
3128 (no) As above, but for split-group #1.
3130 .. mdp:: solvent-group
3132 Name of the index group of solvent molecules.
3134 .. mdp:: coupl-steps
3136 (10) Average the number of ions per compartment over these many swap attempt steps.
3137 This can be used to prevent that ions near a compartment boundary
3138 (diffusing through a channel, e.g.) lead to unwanted back and forth swaps.
3142 (1) The number of different ion types to be controlled. These are during the
3143 simulation exchanged with solvent molecules to reach the desired reference numbers.
3145 .. mdp:: iontype0-name
3147 Name of the first ion type.
3149 .. mdp:: iontype0-in-A
3151 (-1) Requested (=reference) number of ions of type 0 in compartment A.
3152 The default value of -1 means: use the number of ions as found in time step 0
3155 .. mdp:: iontype0-in-B
3157 (-1) Reference number of ions of type 0 for compartment B.
3159 .. mdp:: bulk-offsetA
3161 (0.0) Offset of the first swap layer from the compartment A midplane.
3162 By default (i.e. bulk offset = 0.0), ion/water exchanges happen between layers
3163 at maximum distance (= bulk concentration) to the split group layers. However,
3164 an offset b (-1.0 < b < +1.0) can be specified to offset the bulk layer from the middle at 0.0
3165 towards one of the compartment-partitioning layers (at +/- 1.0).
3167 .. mdp:: bulk-offsetB
3169 (0.0) Offset of the other swap layer from the compartment B midplane.
3174 (\1) Only swap ions if threshold difference to requested count is reached.
3178 (2.0) [nm] Radius of the split cylinder #0.
3179 Two split cylinders (mimicking the channel pores) can optionally be defined
3180 relative to the center of the split group. With the help of these cylinders
3181 it can be counted which ions have passed which channel. The split cylinder
3182 definition has no impact on whether or not ion/water swaps are done.
3186 (1.0) [nm] Upper extension of the split cylinder #0.
3190 (1.0) [nm] Lower extension of the split cylinder #0.
3194 (2.0) [nm] Radius of the split cylinder #1.
3198 (1.0) [nm] Upper extension of the split cylinder #1.
3202 (1.0) [nm] Lower extension of the split cylinder #1.
3204 Density-guided simulations
3205 ^^^^^^^^^^^^^^^^^^^^^^^^^^
3207 These options enable and control the calculation and application of additional
3208 forces that are derived from three-dimensional densities, e.g., from cryo
3209 electron-microscopy experiments. (See the `reference manual`_ for details)
3211 .. mdp:: density-guided-simulation-active
3213 (no) Activate density-guided simulations.
3215 .. mdp:: density-guided-simulation-group
3217 (protein) The atoms that are subject to the forces from the density-guided
3218 simulation and contribute to the simulated density.
3220 .. mdp:: density-guided-simulation-similarity-measure
3222 (inner-product) Similarity measure between the density that is calculated
3223 from the atom positions and the reference density.
3225 .. mdp-value:: inner-product
3227 Takes the sum of the product of reference density and simulated density
3230 .. mdp-value:: relative-entropy
3232 Uses the negative relative entropy (or Kullback-Leibler divergence)
3233 between reference density and simulated density as similarity measure.
3234 Negative density values are ignored.
3236 .. mdp:: density-guided-simulation-atom-spreading-weight
3238 (unity) Determines the multiplication factor for the Gaussian kernel when
3239 spreading atoms on the grid.
3241 .. mdp-value:: unity
3243 Every atom in the density fitting group is assigned the same unit factor.
3247 Atoms contribute to the simulated density proportional to their mass.
3249 .. mdp-value:: charge
3251 Atoms contribute to the simulated density proportional to their charge.
3253 .. mdp:: density-guided-simulation-force-constant
3255 (1e+09) [kJ mol\ :sup:`-1`] The scaling factor for density-guided simulation
3256 forces. May also be negative.
3258 .. mdp:: density-guided-simulation-gaussian-transform-spreading-width
3260 (0.2) [nm] The Gaussian RMS width for the spread kernel for the simulated
3263 .. mdp:: density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width
3265 (4) The range after which the gaussian is cut off in multiples of the Gaussian
3266 RMS width described above.
3268 .. mdp:: density-guided-simulation-reference-density-filename
3270 (reference.mrc) Reference density file name using an absolute path or a path
3271 relative to the to the folder from which :ref:`gmx mdrun` is called.
3273 .. mdp:: density-guided-simulation-nst
3275 (1) Interval in steps at which the density fitting forces are evaluated
3276 and applied. The forces are scaled by this number when applied (See the
3277 `reference manual`_ for details).
3279 .. mdp:: density-guided-simulation-normalize-densities
3281 (true) Normalize the sum of density voxel values to one for the reference
3282 density as well as the simulated density.
3284 .. mdp:: density-guided-simulation-adaptive-force-scaling
3286 (false) Adapt the force constant to ensure a steady increase in similarity
3287 between simulated and reference density.
3291 Do not use adaptive force scaling.
3295 Use adaptive force scaling.
3297 .. mdp:: density-guided-simulation-adaptive-force-scaling-time-constant
3299 (4) [ps] Couple force constant to increase in similarity with reference density
3300 with this time constant. Larger times result in looser coupling.
3302 User defined thingies
3303 ^^^^^^^^^^^^^^^^^^^^^
3307 .. mdp:: userint1 (0)
3308 .. mdp:: userint2 (0)
3309 .. mdp:: userint3 (0)
3310 .. mdp:: userint4 (0)
3311 .. mdp:: userreal1 (0)
3312 .. mdp:: userreal2 (0)
3313 .. mdp:: userreal3 (0)
3314 .. mdp:: userreal4 (0)
3316 These you can use if you modify code. You can pass integers and
3317 reals and groups to your subroutine. Check the inputrec definition
3318 in ``src/gromacs/mdtypes/inputrec.h``
3323 These features have been removed from |Gromacs|, but so that old
3324 :ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
3325 parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
3326 fatal error if this is set.
3332 .. mdp:: implicit-solvent
3336 .. _reference manual: gmx-manual-parent-dir_